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1h4g.cif
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1h4g.cif
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data_1H4G
#
_entry.id 1H4G
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.279
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
PDB 1H4G
PDBE EBI-8019
WWPDB D_1290008019
#
_pdbx_database_related.db_name PDB
_pdbx_database_related.db_id 1H4H
_pdbx_database_related.content_type unspecified
_pdbx_database_related.details
;OLIGOSACCHARIDE-BINDING TO FAMILY 11 XYLANASES: BOTH COVALENT INTERMEDIATE AND MUTANT-PRODUCT COMPLEXES DISPLAY 2,5B CONFORMATIONS AT THE ACTIVE-CENTRE
;
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 1H4G
_pdbx_database_status.deposit_site PDBE
_pdbx_database_status.process_site PDBE
_pdbx_database_status.SG_entry .
_pdbx_database_status.recvd_initial_deposition_date 2001-05-11
_pdbx_database_status.pdb_format_compatible Y
_pdbx_database_status.status_code_sf ?
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.methods_development_category ?
#
loop_
_audit_author.name
_audit_author.pdbx_ordinal
'Sabini, E.' 1
'Wilson, K.S.' 2
'Danielsen, S.' 3
'Schulein, M.' 4
'Davies, G.J.' 5
#
_citation.id primary
_citation.title
;Catalysis and Specificity in Enzymatic Glycoside Hydrolysis: A 2,5B Conformation for the Glycosyl-Enzyme Intermediate Revealed by the Structure of the Bacillus Agaradhaerens Family 11 Xylanase.
;
_citation.journal_abbrev Chem.Biol.
_citation.journal_volume 6
_citation.page_first 483
_citation.page_last ?
_citation.year 1999
_citation.journal_id_ASTM CBOLE2
_citation.country UK
_citation.journal_id_ISSN 1074-5521
_citation.journal_id_CSD 2050
_citation.book_publisher ?
_citation.pdbx_database_id_PubMed 10381409
_citation.pdbx_database_id_DOI '10.1016/S1074-5521(99)80066-0'
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary 'Sabini, E.' 1
primary 'Sulzenbacher, G.' 2
primary 'Dauter, M.' 3
primary 'Dauter, Z.' 4
primary 'Jorgensen, P.L.' 5
primary 'Schulein, M.' 6
primary 'Dupont, C.' 7
primary 'Davies, G.J.' 8
primary 'Wilson, K.S.' 9
#
_cell.entry_id 1H4G
_cell.length_a 72.061
_cell.length_b 75.098
_cell.length_c 78.270
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 90.00
_cell.Z_PDB 8
_cell.pdbx_unique_axis ?
#
_symmetry.entry_id 1H4G
_symmetry.space_group_name_H-M 'P 21 21 21'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 19
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer man XYLANASE 23155.547 2 3.2.1.8 ?
'FAMILY 11 XYLANASE CATALYTIC DOMAIN' '2-FLUORO-2-DEOXY-XYLOBIOSIDE COVALENTLY BOUND TO NUCLEOPHILE GLU94 IN THE ACTIVE SITE'
2 non-polymer man 2-deoxy-2-fluoro-4-O-beta-D-xylopyranosyl-alpha-D-xylopyranose 284.236 2 ? ? ? ?
3 non-polymer syn 'SULFATE ION' 96.063 3 ? ? ? ?
4 water nat water 18.015 606 ? ? ? ?
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer yes
_entity_poly.pdbx_seq_one_letter_code
;(PCA)IVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQP
NGNAYLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGT
ISVSNHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS
;
_entity_poly.pdbx_seq_one_letter_code_can
;EIVTDNSIGNHDGYDYEFWKDSGGSGTMILNHGGTFSAQWNNVNNILFRKGKKFNETQTHQQVGNMSINYGANFQPNGNA
YLCVYGWTVDPLVEYYIVDSWGNWRPPGATPKGTITVDGGTYDIYETLRVNQPSIKGIATFKQYWSVRRSKRTSGTISVS
NHFRAWENLGMNMGKMYEVALTVEGYQSSGSANVYSNTLRINGNPLS
;
_entity_poly.pdbx_strand_id A,B
_entity_poly.pdbx_target_identifier ?
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 PCA n
1 2 ILE n
1 3 VAL n
1 4 THR n
1 5 ASP n
1 6 ASN n
1 7 SER n
1 8 ILE n
1 9 GLY n
1 10 ASN n
1 11 HIS n
1 12 ASP n
1 13 GLY n
1 14 TYR n
1 15 ASP n
1 16 TYR n
1 17 GLU n
1 18 PHE n
1 19 TRP n
1 20 LYS n
1 21 ASP n
1 22 SER n
1 23 GLY n
1 24 GLY n
1 25 SER n
1 26 GLY n
1 27 THR n
1 28 MET n
1 29 ILE n
1 30 LEU n
1 31 ASN n
1 32 HIS n
1 33 GLY n
1 34 GLY n
1 35 THR n
1 36 PHE n
1 37 SER n
1 38 ALA n
1 39 GLN n
1 40 TRP n
1 41 ASN n
1 42 ASN n
1 43 VAL n
1 44 ASN n
1 45 ASN n
1 46 ILE n
1 47 LEU n
1 48 PHE n
1 49 ARG n
1 50 LYS n
1 51 GLY n
1 52 LYS n
1 53 LYS n
1 54 PHE n
1 55 ASN n
1 56 GLU n
1 57 THR n
1 58 GLN n
1 59 THR n
1 60 HIS n
1 61 GLN n
1 62 GLN n
1 63 VAL n
1 64 GLY n
1 65 ASN n
1 66 MET n
1 67 SER n
1 68 ILE n
1 69 ASN n
1 70 TYR n
1 71 GLY n
1 72 ALA n
1 73 ASN n
1 74 PHE n
1 75 GLN n
1 76 PRO n
1 77 ASN n
1 78 GLY n
1 79 ASN n
1 80 ALA n
1 81 TYR n
1 82 LEU n
1 83 CYS n
1 84 VAL n
1 85 TYR n
1 86 GLY n
1 87 TRP n
1 88 THR n
1 89 VAL n
1 90 ASP n
1 91 PRO n
1 92 LEU n
1 93 VAL n
1 94 GLU n
1 95 TYR n
1 96 TYR n
1 97 ILE n
1 98 VAL n
1 99 ASP n
1 100 SER n
1 101 TRP n
1 102 GLY n
1 103 ASN n
1 104 TRP n
1 105 ARG n
1 106 PRO n
1 107 PRO n
1 108 GLY n
1 109 ALA n
1 110 THR n
1 111 PRO n
1 112 LYS n
1 113 GLY n
1 114 THR n
1 115 ILE n
1 116 THR n
1 117 VAL n
1 118 ASP n
1 119 GLY n
1 120 GLY n
1 121 THR n
1 122 TYR n
1 123 ASP n
1 124 ILE n
1 125 TYR n
1 126 GLU n
1 127 THR n
1 128 LEU n
1 129 ARG n
1 130 VAL n
1 131 ASN n
1 132 GLN n
1 133 PRO n
1 134 SER n
1 135 ILE n
1 136 LYS n
1 137 GLY n
1 138 ILE n
1 139 ALA n
1 140 THR n
1 141 PHE n
1 142 LYS n
1 143 GLN n
1 144 TYR n
1 145 TRP n
1 146 SER n
1 147 VAL n
1 148 ARG n
1 149 ARG n
1 150 SER n
1 151 LYS n
1 152 ARG n
1 153 THR n
1 154 SER n
1 155 GLY n
1 156 THR n
1 157 ILE n
1 158 SER n
1 159 VAL n
1 160 SER n
1 161 ASN n
1 162 HIS n
1 163 PHE n
1 164 ARG n
1 165 ALA n
1 166 TRP n
1 167 GLU n
1 168 ASN n
1 169 LEU n
1 170 GLY n
1 171 MET n
1 172 ASN n
1 173 MET n
1 174 GLY n
1 175 LYS n
1 176 MET n
1 177 TYR n
1 178 GLU n
1 179 VAL n
1 180 ALA n
1 181 LEU n
1 182 THR n
1 183 VAL n
1 184 GLU n
1 185 GLY n
1 186 TYR n
1 187 GLN n
1 188 SER n
1 189 SER n
1 190 GLY n
1 191 SER n
1 192 ALA n
1 193 ASN n
1 194 VAL n
1 195 TYR n
1 196 SER n
1 197 ASN n
1 198 THR n
1 199 LEU n
1 200 ARG n
1 201 ILE n
1 202 ASN n
1 203 GLY n
1 204 ASN n
1 205 PRO n
1 206 LEU n
1 207 SER n
#
_entity_src_gen.entity_id 1
_entity_src_gen.pdbx_src_id 1
_entity_src_gen.pdbx_alt_source_flag sample
_entity_src_gen.pdbx_seq_type ?
_entity_src_gen.pdbx_beg_seq_num ?
_entity_src_gen.pdbx_end_seq_num ?
_entity_src_gen.gene_src_common_name ?
_entity_src_gen.gene_src_genus ?
_entity_src_gen.pdbx_gene_src_gene ?
_entity_src_gen.gene_src_species ?
_entity_src_gen.gene_src_strain ?
_entity_src_gen.gene_src_tissue ?
_entity_src_gen.gene_src_tissue_fraction ?
_entity_src_gen.gene_src_details ?
_entity_src_gen.pdbx_gene_src_fragment ?
_entity_src_gen.pdbx_gene_src_scientific_name 'BACILLUS AGARADHAERENS'
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 76935
_entity_src_gen.pdbx_gene_src_variant ?
_entity_src_gen.pdbx_gene_src_cell_line ?
_entity_src_gen.pdbx_gene_src_atcc ?
_entity_src_gen.pdbx_gene_src_organ ?
_entity_src_gen.pdbx_gene_src_organelle ?
_entity_src_gen.pdbx_gene_src_cell ?
_entity_src_gen.pdbx_gene_src_cellular_location ?
_entity_src_gen.host_org_common_name ?
_entity_src_gen.pdbx_host_org_scientific_name 'BACILLUS LICHENIFORMIS'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 1402
_entity_src_gen.host_org_genus ?
_entity_src_gen.pdbx_host_org_gene ?
_entity_src_gen.pdbx_host_org_organ ?
_entity_src_gen.host_org_species ?
_entity_src_gen.pdbx_host_org_tissue ?
_entity_src_gen.pdbx_host_org_tissue_fraction ?
_entity_src_gen.pdbx_host_org_strain ?
_entity_src_gen.pdbx_host_org_variant ?
_entity_src_gen.pdbx_host_org_cell_line ?
_entity_src_gen.pdbx_host_org_atcc ?
_entity_src_gen.pdbx_host_org_culture_collection ?
_entity_src_gen.pdbx_host_org_cell ?
_entity_src_gen.pdbx_host_org_organelle ?
_entity_src_gen.pdbx_host_org_cellular_location ?
_entity_src_gen.pdbx_host_org_vector_type ?
_entity_src_gen.pdbx_host_org_vector ?
_entity_src_gen.host_org_details ?
_entity_src_gen.expression_system_id ?
_entity_src_gen.plasmid_name ?
_entity_src_gen.plasmid_details ?
_entity_src_gen.pdbx_description ?
#
_struct_ref.id 1
_struct_ref.db_name PDB
_struct_ref.db_code 1H4G
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code ?
_struct_ref.pdbx_align_begin ?
_struct_ref.pdbx_db_accession 1H4G
_struct_ref.pdbx_db_isoform ?
#
loop_
_struct_ref_seq.align_id
_struct_ref_seq.ref_id
_struct_ref_seq.pdbx_PDB_id_code
_struct_ref_seq.pdbx_strand_id
_struct_ref_seq.seq_align_beg
_struct_ref_seq.pdbx_seq_align_beg_ins_code
_struct_ref_seq.seq_align_end
_struct_ref_seq.pdbx_seq_align_end_ins_code
_struct_ref_seq.pdbx_db_accession
_struct_ref_seq.db_align_beg
_struct_ref_seq.pdbx_db_align_beg_ins_code
_struct_ref_seq.db_align_end
_struct_ref_seq.pdbx_db_align_end_ins_code
_struct_ref_seq.pdbx_auth_seq_align_beg
_struct_ref_seq.pdbx_auth_seq_align_end
1 1 1H4G A 1 ? 207 ? 1H4G 1 ? 207 ? 1 207
2 1 1H4G B 1 ? 207 ? 1H4G 1 ? 207 ? 1 207
#
loop_
_struct_ref_seq_dif.align_id
_struct_ref_seq_dif.pdbx_pdb_id_code
_struct_ref_seq_dif.mon_id
_struct_ref_seq_dif.pdbx_pdb_strand_id
_struct_ref_seq_dif.seq_num
_struct_ref_seq_dif.pdbx_pdb_ins_code
_struct_ref_seq_dif.pdbx_seq_db_name
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_ref_seq_dif.db_mon_id
_struct_ref_seq_dif.pdbx_seq_db_seq_num
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_auth_seq_num
_struct_ref_seq_dif.pdbx_ordinal
1 1H4G PCA A 1 ? PDB 1H4G GLU 1 'modified residue' 1 1
2 1H4G PCA B 1 ? PDB 1H4G GLU 1 'modified residue' 1 2
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093
ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118
ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103
CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158
FXP D-saccharide . 2-deoxy-2-fluoro-4-O-beta-D-xylopyranosyl-alpha-D-xylopyranose ? 'C10 H17 F O8' 284.236
GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144
GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129
GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067
HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162
HOH non-polymer . WATER ? 'H2 O' 18.015
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173
LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195
MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211
PCA 'L-peptide linking' n 'PYROGLUTAMIC ACID' ? 'C5 H7 N O3' 129.114
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063
THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119
TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225
TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146
#
_exptl.entry_id 1H4G
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 2.6
_exptl_crystal.density_percent_sol 53
_exptl_crystal.description ?
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method ?
_exptl_crystal_grow.temp ?
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pH 6.00
_exptl_crystal_grow.pdbx_pH_range ?
_exptl_crystal_grow.pdbx_details
'DROP: 2UL PROTEIN (10 MG ML-1 IN 100MM SODIUM ACETATE) PLUS 1UL RESERVOIR RESERVOIR: 100 MM MES PH 6.5, 30% AMMONIUM SULPHATE'
#
_diffrn.id 1
_diffrn.ambient_temp 120.0
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.monochromator ?
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 0.8469
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source SYNCHROTRON
_diffrn_source.type 'EMBL/DESY, HAMBURG BEAMLINE BW7B'
_diffrn_source.pdbx_synchrotron_site 'EMBL/DESY, Hamburg'
_diffrn_source.pdbx_synchrotron_beamline BW7B
_diffrn_source.pdbx_wavelength 0.8469
_diffrn_source.pdbx_wavelength_list ?
#
_reflns.pdbx_diffrn_id 1
_reflns.pdbx_ordinal 1
_reflns.entry_id 1H4G
_reflns.observed_criterion_sigma_I 2.000
_reflns.observed_criterion_sigma_F ?
_reflns.d_resolution_low 20.000
_reflns.d_resolution_high 1.100
_reflns.number_obs 171783
_reflns.number_all ?
_reflns.percent_possible_obs 99.8
_reflns.pdbx_Rmerge_I_obs 0.07000
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 17.6000
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy 4.500
#
_reflns_shell.pdbx_diffrn_id 1
_reflns_shell.pdbx_ordinal 1
_reflns_shell.d_res_high 1.10
_reflns_shell.d_res_low 1.12
_reflns_shell.percent_possible_all 99.0
_reflns_shell.Rmerge_I_obs 0.70800
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs 2.000
_reflns_shell.pdbx_redundancy 3.80
#
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.entry_id 1H4G
_refine.pdbx_diffrn_id 1
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.ls_number_reflns_obs 171783
_refine.ls_number_reflns_all ?
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F ?
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.ls_d_res_low 20.0
_refine.ls_d_res_high 1.10
_refine.ls_percent_reflns_obs 99.8
_refine.ls_R_factor_obs ?
_refine.ls_R_factor_all ?
_refine.ls_R_factor_R_work 0.158
_refine.ls_R_factor_R_free 0.181
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_percent_reflns_R_free 5.0
_refine.ls_number_reflns_R_free ?
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.occupancy_min ?
_refine.occupancy_max ?
_refine.correlation_coeff_Fo_to_Fc ?
_refine.correlation_coeff_Fo_to_Fc_free ?
_refine.B_iso_mean ?
_refine.aniso_B[1][1] ?
_refine.aniso_B[2][2] ?
_refine.aniso_B[3][3] ?
_refine.aniso_B[1][2] ?
_refine.aniso_B[1][3] ?
_refine.aniso_B[2][3] ?
_refine.solvent_model_details ?
_refine.solvent_model_param_ksol ?
_refine.solvent_model_param_bsol ?
_refine.pdbx_solvent_vdw_probe_radii ?
_refine.pdbx_solvent_ion_probe_radii ?
_refine.pdbx_solvent_shrinkage_radii ?
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.details ?
_refine.pdbx_starting_model ?
_refine.pdbx_method_to_determine_struct OTHER
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_stereochemistry_target_values ?
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_R_Free_selection_details RANDOM
_refine.pdbx_overall_ESU_R ?
_refine.pdbx_overall_ESU_R_Free 0.03143
_refine.overall_SU_ML 0.01943
_refine.pdbx_overall_phase_error ?
_refine.overall_SU_B 0.38942
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 3263
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 51
_refine_hist.number_atoms_solvent 606
_refine_hist.number_atoms_total 3920
_refine_hist.d_res_high 1.10
_refine_hist.d_res_low 20.0
#
_struct.entry_id 1H4G
_struct.title
;Oligosaccharide-binding to family 11 xylanases: both covalent intermediate and mutant-product complexes display 2,5B conformations at the active-centre
;
_struct.pdbx_descriptor 'XYLANASE (E.C.3.2.1.8)'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 1H4G
_struct_keywords.pdbx_keywords 'GLYCOSIDE HYDROLASE'
_struct_keywords.text
'GLYCOSIDE HYDROLASE, XYLANASE, OLIGOSACCHARIDE, TRANSITION-STATE, INTERMEDIATE, MUTANT, BOAT CONFORMATION'
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 1 ?
C N N 2 ?
D N N 3 ?
E N N 2 ?
F N N 3 ?
G N N 3 ?
H N N 4 ?
I N N 4 ?
#
_struct_biol.id 1
#
loop_
_struct_conf.conf_type_id
_struct_conf.id
_struct_conf.pdbx_PDB_helix_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.pdbx_beg_PDB_ins_code
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.pdbx_end_PDB_ins_code
_struct_conf.beg_auth_comp_id
_struct_conf.beg_auth_asym_id
_struct_conf.beg_auth_seq_id
_struct_conf.end_auth_comp_id
_struct_conf.end_auth_asym_id
_struct_conf.end_auth_seq_id
_struct_conf.pdbx_PDB_helix_class
_struct_conf.details
_struct_conf.pdbx_PDB_helix_length
HELX_P HELX_P1 1 THR A 59 ? GLY A 64 ? THR A 59 GLY A 64 1 ? 6
HELX_P HELX_P2 2 SER A 158 ? LEU A 169 ? SER A 158 LEU A 169 1 ? 12
HELX_P HELX_P3 1 THR B 59 ? GLY B 64 ? THR B 59 GLY B 64 1 ? 6
HELX_P HELX_P4 2 SER B 158 ? LEU B 169 ? SER B 158 LEU B 169 1 ? 12
#
_struct_conf_type.id HELX_P
_struct_conf_type.criteria ?
_struct_conf_type.reference ?
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
covale1 covale ? ? A PCA 1 C ? ? ? 1_555 A ILE 2 N ? ? A PCA 1 A ILE 2 1_555 ? ? ? ? ? ? ? 1.380 ?
covale2 covale ? ? A GLU 94 OE2 ? ? ? 1_555 C FXP . C1A ? ? A GLU 94 A FXP 1207 1_555 ? ? ? ? ? ? ? 1.482 ?
covale3 covale ? ? B PCA 1 C ? ? ? 1_555 B ILE 2 N ? ? B PCA 1 B ILE 2 1_555 ? ? ? ? ? ? ? 1.432 ?
covale4 covale ? ? B GLU 94 OE2 ? ? ? 1_555 E FXP . C1A ? ? B GLU 94 B FXP 1208 1_555 ? ? ? ? ? ? ? 1.506 ?
#
_struct_conn_type.id covale
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
loop_
_struct_mon_prot_cis.pdbx_id
_struct_mon_prot_cis.label_comp_id
_struct_mon_prot_cis.label_seq_id
_struct_mon_prot_cis.label_asym_id
_struct_mon_prot_cis.label_alt_id
_struct_mon_prot_cis.pdbx_PDB_ins_code
_struct_mon_prot_cis.auth_comp_id
_struct_mon_prot_cis.auth_seq_id
_struct_mon_prot_cis.auth_asym_id
_struct_mon_prot_cis.pdbx_label_comp_id_2
_struct_mon_prot_cis.pdbx_label_seq_id_2
_struct_mon_prot_cis.pdbx_label_asym_id_2
_struct_mon_prot_cis.pdbx_PDB_ins_code_2
_struct_mon_prot_cis.pdbx_auth_comp_id_2
_struct_mon_prot_cis.pdbx_auth_seq_id_2
_struct_mon_prot_cis.pdbx_auth_asym_id_2
_struct_mon_prot_cis.pdbx_PDB_model_num
_struct_mon_prot_cis.pdbx_omega_angle
1 ASP 90 A . ? ASP 90 A PRO 91 A ? PRO 91 A 1 6.44
2 PRO 106 A . ? PRO 106 A PRO 107 A ? PRO 107 A 1 3.41
3 ASP 90 B . ? ASP 90 B PRO 91 B ? PRO 91 B 1 7.93
4 PRO 106 B . ? PRO 106 B PRO 107 B ? PRO 107 B 1 -0.42
#
loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
AA ? 5 ?
AB ? 4 ?
AC ? 9 ?
BA ? 5 ?
BB ? 4 ?
BC ? 9 ?
#
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
AA 1 2 ? anti-parallel
AA 2 3 ? anti-parallel
AA 3 4 ? anti-parallel
AA 4 5 ? anti-parallel
AB 1 2 ? anti-parallel
AB 2 3 ? anti-parallel
AB 3 4 ? anti-parallel
AC 1 2 ? anti-parallel
AC 2 3 ? anti-parallel
AC 3 4 ? anti-parallel
AC 4 5 ? anti-parallel
AC 5 6 ? anti-parallel
AC 6 7 ? parallel
AC 7 8 ? anti-parallel
AC 8 9 ? anti-parallel
BA 1 2 ? anti-parallel
BA 2 3 ? anti-parallel
BA 3 4 ? anti-parallel
BA 4 5 ? anti-parallel
BB 1 2 ? anti-parallel
BB 2 3 ? anti-parallel
BB 3 4 ? anti-parallel
BC 1 2 ? anti-parallel
BC 2 3 ? anti-parallel
BC 3 4 ? anti-parallel
BC 4 5 ? anti-parallel
BC 5 6 ? anti-parallel
BC 6 7 ? parallel
BC 7 8 ? anti-parallel
BC 8 9 ? anti-parallel
#
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.pdbx_beg_PDB_ins_code
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.pdbx_end_PDB_ins_code
_struct_sheet_range.beg_auth_comp_id
_struct_sheet_range.beg_auth_asym_id
_struct_sheet_range.beg_auth_seq_id
_struct_sheet_range.end_auth_comp_id
_struct_sheet_range.end_auth_asym_id
_struct_sheet_range.end_auth_seq_id
AA 1 ILE A 2 ? VAL A 3 ? ILE A 2 VAL A 3
AA 2 SER A 25 ? LEU A 30 ? SER A 25 LEU A 30
AA 3 PHE A 36 ? ASN A 41 ? PHE A 36 ASN A 41
AA 4 GLY A 190 ? VAL A 194 ? GLY A 190 VAL A 194
AA 5 GLN A 75 ? PRO A 76 ? GLN A 75 PRO A 76
AB 1 GLY A 155 ? ILE A 157 ? GLY A 155 ILE A 157
AB 2 MET A 66 ? TYR A 70 ? MET A 66 TYR A 70
AB 3 THR A 198 ? ILE A 201 ? THR A 198 ILE A 201
AB 4 ASN A 204 ? PRO A 205 ? ASN A 204 PRO A 205
AC 1 SER A 7 ? HIS A 11 ? SER A 7 HIS A 11
AC 2 TYR A 14 ? LYS A 20 ? TYR A 14 LYS A 20
AC 3 ASN A 45 ? LYS A 53 ? ASN A 45 LYS A 53
AC 4 LYS A 175 ? TYR A 186 ? LYS A 175 TYR A 186
AC 5 ALA A 80 ? VAL A 89 ? ALA A 80 VAL A 89
AC 6 VAL A 93 ? TRP A 101 ? VAL A 93 TRP A 101
AC 7 ALA A 139 ? ARG A 148 ? ALA A 139 ARG A 148
AC 8 GLY A 120 ? GLN A 132 ? GLY A 120 GLN A 132
AC 9 GLY A 113 ? VAL A 117 ? GLY A 113 VAL A 117
BA 1 ILE B 2 ? VAL B 3 ? ILE B 2 VAL B 3
BA 2 SER B 25 ? LEU B 30 ? SER B 25 LEU B 30
BA 3 PHE B 36 ? ASN B 41 ? PHE B 36 ASN B 41
BA 4 GLY B 190 ? VAL B 194 ? GLY B 190 VAL B 194
BA 5 GLN B 75 ? PRO B 76 ? GLN B 75 PRO B 76
BB 1 GLY B 155 ? ILE B 157 ? GLY B 155 ILE B 157
BB 2 MET B 66 ? TYR B 70 ? MET B 66 TYR B 70
BB 3 THR B 198 ? ILE B 201 ? THR B 198 ILE B 201
BB 4 ASN B 204 ? PRO B 205 ? ASN B 204 PRO B 205
BC 1 SER B 7 ? HIS B 11 ? SER B 7 HIS B 11
BC 2 TYR B 14 ? LYS B 20 ? TYR B 14 LYS B 20
BC 3 ASN B 45 ? LYS B 53 ? ASN B 45 LYS B 53
BC 4 LYS B 175 ? TYR B 186 ? LYS B 175 TYR B 186
BC 5 ALA B 80 ? VAL B 89 ? ALA B 80 VAL B 89
BC 6 VAL B 93 ? TRP B 101 ? VAL B 93 TRP B 101
BC 7 ALA B 139 ? ARG B 148 ? ALA B 139 ARG B 148
BC 8 GLY B 120 ? GLN B 132 ? GLY B 120 GLN B 132
BC 9 GLY B 113 ? VAL B 117 ? GLY B 113 VAL B 117
#
loop_
_pdbx_struct_sheet_hbond.sheet_id
_pdbx_struct_sheet_hbond.range_id_1
_pdbx_struct_sheet_hbond.range_id_2
_pdbx_struct_sheet_hbond.range_1_label_atom_id
_pdbx_struct_sheet_hbond.range_1_label_comp_id
_pdbx_struct_sheet_hbond.range_1_label_asym_id
_pdbx_struct_sheet_hbond.range_1_label_seq_id
_pdbx_struct_sheet_hbond.range_1_PDB_ins_code
_pdbx_struct_sheet_hbond.range_1_auth_atom_id
_pdbx_struct_sheet_hbond.range_1_auth_comp_id
_pdbx_struct_sheet_hbond.range_1_auth_asym_id
_pdbx_struct_sheet_hbond.range_1_auth_seq_id
_pdbx_struct_sheet_hbond.range_2_label_atom_id
_pdbx_struct_sheet_hbond.range_2_label_comp_id
_pdbx_struct_sheet_hbond.range_2_label_asym_id
_pdbx_struct_sheet_hbond.range_2_label_seq_id
_pdbx_struct_sheet_hbond.range_2_PDB_ins_code
_pdbx_struct_sheet_hbond.range_2_auth_atom_id
_pdbx_struct_sheet_hbond.range_2_auth_comp_id
_pdbx_struct_sheet_hbond.range_2_auth_asym_id
_pdbx_struct_sheet_hbond.range_2_auth_seq_id
AA 1 2 N VAL A 3 ? N VAL A 3 O MET A 28 ? O MET A 28
AA 2 3 N ILE A 29 ? N ILE A 29 O SER A 37 ? O SER A 37
AA 3 4 N TRP A 40 ? N TRP A 40 O GLY A 190 ? O GLY A 190
AA 4 5 N SER A 191 ? N SER A 191 O GLN A 75 ? O GLN A 75
AB 1 2 N ILE A 157 ? N ILE A 157 O ILE A 68 ? O ILE A 68
AB 2 3 N ASN A 69 ? N ASN A 69 O THR A 198 ? O THR A 198
AB 3 4 N ILE A 201 ? N ILE A 201 O ASN A 204 ? O ASN A 204
AC 1 2 N HIS A 11 ? N HIS A 11 O TYR A 14 ? O TYR A 14
AC 2 3 N TRP A 19 ? N TRP A 19 O LEU A 47 ? O LEU A 47
AC 3 4 N LYS A 52 ? N LYS A 52 O VAL A 179 ? O VAL A 179
AC 4 5 N GLU A 184 ? N GLU A 184 O TYR A 81 ? O TYR A 81
AC 5 6 N THR A 88 ? N THR A 88 O VAL A 93 ? O VAL A 93
AC 6 7 N GLU A 94 ? N GLU A 94 O LYS A 142 ? O LYS A 142
AC 7 8 N VAL A 147 ? N VAL A 147 O ASP A 123 ? O ASP A 123
AC 8 9 N ILE A 124 ? N ILE A 124 O GLY A 113 ? O GLY A 113
BA 1 2 N VAL B 3 ? N VAL B 3 O MET B 28 ? O MET B 28
BA 2 3 N ILE B 29 ? N ILE B 29 O SER B 37 ? O SER B 37
BA 3 4 N TRP B 40 ? N TRP B 40 O GLY B 190 ? O GLY B 190
BA 4 5 N SER B 191 ? N SER B 191 O GLN B 75 ? O GLN B 75
BB 1 2 N ILE B 157 ? N ILE B 157 O ILE B 68 ? O ILE B 68
BB 2 3 N ASN B 69 ? N ASN B 69 O THR B 198 ? O THR B 198
BB 3 4 N ILE B 201 ? N ILE B 201 O ASN B 204 ? O ASN B 204
BC 1 2 N HIS B 11 ? N HIS B 11 O TYR B 14 ? O TYR B 14
BC 2 3 N TRP B 19 ? N TRP B 19 O LEU B 47 ? O LEU B 47
BC 3 4 N LYS B 52 ? N LYS B 52 O VAL B 179 ? O VAL B 179
BC 4 5 N GLU B 184 ? N GLU B 184 O TYR B 81 ? O TYR B 81
BC 5 6 N THR B 88 ? N THR B 88 O VAL B 93 ? O VAL B 93
BC 6 7 N GLU B 94 ? N GLU B 94 O LYS B 142 ? O LYS B 142
BC 7 8 N VAL B 147 ? N VAL B 147 O ASP B 123 ? O ASP B 123
BC 8 9 N ILE B 124 ? N ILE B 124 O GLY B 113 ? O GLY B 113
#
loop_
_struct_site.id
_struct_site.pdbx_evidence_code
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_struct_site.pdbx_auth_ins_code
_struct_site.pdbx_num_residues
_struct_site.details
AC1 Software ? ? ? ? 15 'BINDING SITE FOR RESIDUE FXP A1207'
AC2 Software ? ? ? ? 15 'BINDING SITE FOR RESIDUE FXP B1208'
AC3 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE SO4 A1208'
AC4 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE SO4 B1209'
AC5 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE SO4 B1210'
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 15 GLU A 17 ? GLU A 17 . ? 1_555 ?
2 AC1 15 TRP A 19 ? TRP A 19 . ? 1_555 ?
3 AC1 15 LEU A 47 ? LEU A 47 . ? 1_555 ?
4 AC1 15 ARG A 49 ? ARG A 49 . ? 1_555 ?
5 AC1 15 TYR A 85 ? TYR A 85 . ? 1_555 ?
6 AC1 15 TRP A 87 ? TRP A 87 . ? 1_555 ?
7 AC1 15 GLU A 94 ? GLU A 94 . ? 1_555 ?
8 AC1 15 TYR A 96 ? TYR A 96 . ? 1_555 ?
9 AC1 15 ARG A 129 ? ARG A 129 . ? 1_555 ?
10 AC1 15 PRO A 133 ? PRO A 133 . ? 1_555 ?
11 AC1 15 SER A 134 ? SER A 134 . ? 1_555 ?
12 AC1 15 PHE A 141 ? PHE A 141 . ? 1_555 ?
13 AC1 15 GLN A 143 ? GLN A 143 . ? 1_555 ?
14 AC1 15 HOH H . ? HOH A 2315 . ? 1_555 ?
15 AC1 15 HOH H . ? HOH A 2316 . ? 1_555 ?
16 AC2 15 GLU B 17 ? GLU B 17 . ? 1_555 ?
17 AC2 15 TRP B 19 ? TRP B 19 . ? 1_555 ?
18 AC2 15 LEU B 47 ? LEU B 47 . ? 1_555 ?
19 AC2 15 ARG B 49 ? ARG B 49 . ? 1_555 ?
20 AC2 15 TYR B 85 ? TYR B 85 . ? 1_555 ?
21 AC2 15 TRP B 87 ? TRP B 87 . ? 1_555 ?
22 AC2 15 GLU B 94 ? GLU B 94 . ? 1_555 ?
23 AC2 15 TYR B 96 ? TYR B 96 . ? 1_555 ?
24 AC2 15 ARG B 129 ? ARG B 129 . ? 1_555 ?
25 AC2 15 PRO B 133 ? PRO B 133 . ? 1_555 ?
26 AC2 15 SER B 134 ? SER B 134 . ? 1_555 ?
27 AC2 15 PHE B 141 ? PHE B 141 . ? 1_555 ?
28 AC2 15 GLN B 143 ? GLN B 143 . ? 1_555 ?
29 AC2 15 HOH I . ? HOH B 2284 . ? 1_555 ?
30 AC2 15 HOH I . ? HOH B 2285 . ? 1_555 ?
31 AC3 6 ARG A 152 ? ARG A 152 . ? 1_555 ?
32 AC3 6 THR A 153 ? THR A 153 . ? 1_555 ?
33 AC3 6 HOH H . ? HOH A 2252 . ? 1_555 ?
34 AC3 6 HOH H . ? HOH A 2317 . ? 1_555 ?
35 AC3 6 HOH H . ? HOH A 2318 . ? 1_555 ?
36 AC3 6 HOH H . ? HOH A 2319 . ? 1_555 ?
37 AC4 6 ARG B 152 ? ARG B 152 . ? 1_555 ?
38 AC4 6 THR B 153 ? THR B 153 . ? 1_555 ?
39 AC4 6 HOH I . ? HOH B 2223 . ? 1_555 ?
40 AC4 6 HOH I . ? HOH B 2224 . ? 1_555 ?
41 AC4 6 HOH I . ? HOH B 2286 . ? 1_555 ?
42 AC4 6 HOH I . ? HOH B 2287 . ? 1_555 ?
43 AC5 4 ASN B 69 ? ASN B 69 . ? 1_555 ?
44 AC5 4 THR B 198 ? THR B 198 . ? 1_555 ?
45 AC5 4 ARG B 200 ? ARG B 200 . ? 1_555 ?
46 AC5 4 HOH I . ? HOH B 2271 . ? 1_555 ?
#
_database_PDB_matrix.entry_id 1H4G
_database_PDB_matrix.origx[1][1] 1.000000
_database_PDB_matrix.origx[1][2] 0.000000
_database_PDB_matrix.origx[1][3] 0.000000
_database_PDB_matrix.origx[2][1] 0.000000
_database_PDB_matrix.origx[2][2] 1.000000
_database_PDB_matrix.origx[2][3] 0.000000
_database_PDB_matrix.origx[3][1] 0.000000
_database_PDB_matrix.origx[3][2] 0.000000
_database_PDB_matrix.origx[3][3] 1.000000
_database_PDB_matrix.origx_vector[1] 0.00000
_database_PDB_matrix.origx_vector[2] 0.00000
_database_PDB_matrix.origx_vector[3] 0.00000
#
_atom_sites.entry_id 1H4G
_atom_sites.fract_transf_matrix[1][1] 0.013877
_atom_sites.fract_transf_matrix[1][2] 0.000000
_atom_sites.fract_transf_matrix[1][3] 0.000000
_atom_sites.fract_transf_matrix[2][1] 0.000000
_atom_sites.fract_transf_matrix[2][2] 0.013316
_atom_sites.fract_transf_matrix[2][3] 0.000000
_atom_sites.fract_transf_matrix[3][1] 0.000000
_atom_sites.fract_transf_matrix[3][2] 0.000000
_atom_sites.fract_transf_matrix[3][3] 0.012776
_atom_sites.fract_transf_vector[1] 0.00000
_atom_sites.fract_transf_vector[2] 0.00000
_atom_sites.fract_transf_vector[3] 0.00000
#
loop_
_atom_type.symbol
C
F
N
O
S