data_1V7H # _entry.id 1V7H # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.389 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 1V7H pdb_00001v7h 10.2210/pdb1v7h/pdb RCSB RCSB006302 ? ? WWPDB D_1000006302 ? ? # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2004-08-03 2 'Structure model' 1 1 2008-04-27 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2013-12-25 5 'Structure model' 1 4 2023-12-27 6 'Structure model' 1 5 2024-04-03 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Version format compliance' 3 4 'Structure model' 'Derived calculations' 4 5 'Structure model' 'Data collection' 5 5 'Structure model' 'Database references' 6 5 'Structure model' 'Derived calculations' 7 6 'Structure model' 'Refinement description' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 5 'Structure model' chem_comp_atom 2 5 'Structure model' chem_comp_bond 3 5 'Structure model' database_2 4 5 'Structure model' struct_conn 5 6 'Structure model' pdbx_initial_refinement_model # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 5 'Structure model' '_database_2.pdbx_DOI' 2 5 'Structure model' '_database_2.pdbx_database_accession' 3 5 'Structure model' '_struct_conn.pdbx_dist_value' 4 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 5 5 'Structure model' '_struct_conn.ptnr1_auth_asym_id' 6 5 'Structure model' '_struct_conn.ptnr1_auth_comp_id' 7 5 'Structure model' '_struct_conn.ptnr1_auth_seq_id' 8 5 'Structure model' '_struct_conn.ptnr1_label_asym_id' 9 5 'Structure model' '_struct_conn.ptnr1_label_atom_id' 10 5 'Structure model' '_struct_conn.ptnr1_label_comp_id' 11 5 'Structure model' '_struct_conn.ptnr1_label_seq_id' 12 5 'Structure model' '_struct_conn.ptnr1_symmetry' 13 5 'Structure model' '_struct_conn.ptnr2_auth_asym_id' 14 5 'Structure model' '_struct_conn.ptnr2_auth_comp_id' 15 5 'Structure model' '_struct_conn.ptnr2_auth_seq_id' 16 5 'Structure model' '_struct_conn.ptnr2_label_asym_id' 17 5 'Structure model' '_struct_conn.ptnr2_label_atom_id' 18 5 'Structure model' '_struct_conn.ptnr2_label_comp_id' 19 5 'Structure model' '_struct_conn.ptnr2_label_seq_id' 20 5 'Structure model' '_struct_conn.ptnr2_symmetry' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1V7H _pdbx_database_status.recvd_initial_deposition_date 2003-12-17 _pdbx_database_status.deposit_site PDBJ _pdbx_database_status.process_site PDBJ _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1CAG 'Similar sequence' unspecified PDB 1V4F 'The same sequence and measured temperature with different chain length' unspecified PDB 1V6Q 'The peptide with the same sequence and different chain length measured at RT' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Okuyama, K.' 1 'Hongo, C.' 2 'Fukushima, R.' 3 'Wu, G.' 4 'Narita, H.' 5 'Noguchi, K.' 6 'Tanaka, Y.' 7 'Nishino, N.' 8 # _citation.id primary _citation.title ;Crystal structures of collagen model peptides with Pro-Hyp-Gly repeating sequence at 1.26 A resolution: implications for proline ring puckering ; _citation.journal_abbrev Biopolymers _citation.journal_volume 76 _citation.page_first 367 _citation.page_last 377 _citation.year 2004 _citation.journal_id_ASTM BIPMAA _citation.country US _citation.journal_id_ISSN 0006-3525 _citation.journal_id_CSD 0161 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 15386273 _citation.pdbx_database_id_DOI 10.1002/bip.20107 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Okuyama, K.' 1 ? primary 'Hongo, C.' 2 ? primary 'Fukushima, R.' 3 ? primary 'Wu, G.' 4 ? primary 'Narita, H.' 5 ? primary 'Noguchi, K.' 6 ? primary 'Tanaka, Y.' 7 ? primary 'Nishino, N.' 8 ? # 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 syn 'Collagen like peptide' 609.630 1 ? ? ? ? 2 polymer syn 'Collagen like peptide' 665.693 1 ? ? ? ? 3 polymer syn 'Collagen like peptide' 649.693 1 ? ? ? ? 4 water nat water 18.015 49 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no yes 'GP(HYP)GP(HYP)G' GPPGPPG A ? 2 'polypeptide(L)' no yes '(HYP)GP(HYP)GP(HYP)' PGPPGPP B ? 3 'polypeptide(L)' no yes 'P(HYP)GP(HYP)GP' PPGPPGP C ? # _pdbx_entity_nonpoly.entity_id 4 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 PRO n 1 3 HYP n 1 4 GLY n 1 5 PRO n 1 6 HYP n 1 7 GLY n 2 1 HYP n 2 2 GLY n 2 3 PRO n 2 4 HYP n 2 5 GLY n 2 6 PRO n 2 7 HYP n 3 1 PRO n 3 2 HYP n 3 3 GLY n 3 4 PRO n 3 5 HYP n 3 6 GLY n 3 7 PRO n # loop_ _pdbx_entity_src_syn.entity_id _pdbx_entity_src_syn.pdbx_src_id _pdbx_entity_src_syn.pdbx_alt_source_flag _pdbx_entity_src_syn.pdbx_beg_seq_num _pdbx_entity_src_syn.pdbx_end_seq_num _pdbx_entity_src_syn.organism_scientific _pdbx_entity_src_syn.organism_common_name _pdbx_entity_src_syn.ncbi_taxonomy_id _pdbx_entity_src_syn.details 1 1 sample ? ? ? ? ? 'Pro-Hyp-Gly triplet is very popular in collagen sequence' 2 1 sample ? ? ? ? ? 'Pro-Hyp-Gly triplet is very popular in collagen sequence' 3 1 sample ? ? ? ? ? 'Pro-Hyp-Gly triplet is very popular in collagen sequence' # 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 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 HYP 'L-peptide linking' n 4-HYDROXYPROLINE HYDROXYPROLINE 'C5 H9 N O3' 131.130 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 1 1 GLY GLY A . n A 1 2 PRO 2 2 2 PRO PRO A . n A 1 3 HYP 3 3 3 HYP HYP A . n A 1 4 GLY 4 4 4 GLY GLY A . n A 1 5 PRO 5 5 5 PRO PRO A . n A 1 6 HYP 6 6 6 HYP HYP A . n A 1 7 GLY 7 7 7 GLY GLY A . n B 2 1 HYP 1 1 1 HYP HYP B . n B 2 2 GLY 2 2 2 GLY GLY B . n B 2 3 PRO 3 3 3 PRO PRO B . n B 2 4 HYP 4 4 4 HYP HYP B . n B 2 5 GLY 5 5 5 GLY GLY B . n B 2 6 PRO 6 6 6 PRO PRO B . n B 2 7 HYP 7 7 7 HYP HYP B . n C 3 1 PRO 1 1 1 PRO PRO C . n C 3 2 HYP 2 2 2 HYP HYP C . n C 3 3 GLY 3 3 3 GLY GLY C . n C 3 4 PRO 4 4 4 PRO PRO C . n C 3 5 HYP 5 5 5 HYP HYP C . n C 3 6 GLY 6 6 6 GLY GLY C . n C 3 7 PRO 7 7 7 PRO PRO C . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code D 4 HOH 1 8 2 HOH HOH A . D 4 HOH 2 9 4 HOH HOH A . D 4 HOH 3 10 5 HOH HOH A . D 4 HOH 4 11 8 HOH HOH A . D 4 HOH 5 12 12 HOH HOH A . D 4 HOH 6 13 13 HOH HOH A . D 4 HOH 7 14 16 HOH HOH A . D 4 HOH 8 15 18 HOH HOH A . D 4 HOH 9 16 20 HOH HOH A . D 4 HOH 10 17 21 HOH HOH A . D 4 HOH 11 18 22 HOH HOH A . D 4 HOH 12 19 23 HOH HOH A . D 4 HOH 13 20 26 HOH HOH A . D 4 HOH 14 21 31 HOH HOH A . D 4 HOH 15 22 38 HOH HOH A . D 4 HOH 16 23 39 HOH HOH A . D 4 HOH 17 24 46 HOH HOH A . E 4 HOH 1 8 1 HOH HOH B . E 4 HOH 2 9 7 HOH HOH B . E 4 HOH 3 10 10 HOH HOH B . E 4 HOH 4 11 15 HOH HOH B . E 4 HOH 5 12 19 HOH HOH B . E 4 HOH 6 13 24 HOH HOH B . E 4 HOH 7 14 28 HOH HOH B . E 4 HOH 8 15 32 HOH HOH B . E 4 HOH 9 16 34 HOH HOH B . E 4 HOH 10 17 37 HOH HOH B . E 4 HOH 11 18 40 HOH HOH B . E 4 HOH 12 19 41 HOH HOH B . E 4 HOH 13 20 43 HOH HOH B . E 4 HOH 14 21 47 HOH HOH B . E 4 HOH 15 22 48 HOH HOH B . E 4 HOH 16 23 49 HOH HOH B . F 4 HOH 1 8 3 HOH HOH C . F 4 HOH 2 9 6 HOH HOH C . F 4 HOH 3 10 9 HOH HOH C . F 4 HOH 4 11 11 HOH HOH C . F 4 HOH 5 12 14 HOH HOH C . F 4 HOH 6 13 17 HOH HOH C . F 4 HOH 7 14 25 HOH HOH C . F 4 HOH 8 15 27 HOH HOH C . F 4 HOH 9 16 29 HOH HOH C . F 4 HOH 10 17 30 HOH HOH C . F 4 HOH 11 18 33 HOH HOH C . F 4 HOH 12 19 35 HOH HOH C . F 4 HOH 13 20 36 HOH HOH C . F 4 HOH 14 21 42 HOH HOH C . F 4 HOH 15 22 44 HOH HOH C . F 4 HOH 16 23 45 HOH HOH C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHELX 'model building' . ? 1 SHELXL-97 refinement . ? 2 CrystalClear 'data reduction' . ? 3 CrystalClear 'data scaling' '(MSC/RIGAKU)' ? 4 SHELXS phasing . ? 5 # _cell.entry_id 1V7H _cell.length_a 13.892 _cell.length_b 26.115 _cell.length_c 19.954 _cell.angle_alpha 90.00 _cell.angle_beta 105.95 _cell.angle_gamma 90.00 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 1V7H _symmetry.space_group_name_H-M 'P 1 21 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? # _exptl.entry_id 1V7H _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.81 _exptl_crystal.density_percent_sol 31.96 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 283 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'PEG200, ACETIC ACID, VAPOR DIFFUSION, HANGING DROP, temperature 283K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'OXFORD PX210' _diffrn_detector.pdbx_collection_date 2002-06-11 _diffrn_detector.details MIRROR-MONOCHROMATOR # _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 0.9 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL44XU' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL44XU _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.9 # _reflns.entry_id 1V7H _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 1.0 _reflns.d_resolution_low 20.0 _reflns.d_resolution_high 1.24 _reflns.number_obs 3257 _reflns.number_all ? _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs 0.042 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # _reflns_shell.d_res_high 1.24 _reflns_shell.d_res_low 1.28 _reflns_shell.percent_possible_all 74 _reflns_shell.Rmerge_I_obs 0.057 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 8.2 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 290 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 1V7H _refine.ls_number_reflns_obs 3173 _refine.ls_number_reflns_all 3176 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 4.0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 10.00 _refine.ls_d_res_high 1.25 _refine.ls_percent_reflns_obs 78.2 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1271 _refine.ls_R_factor_R_free 0.1828 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.7 _refine.ls_number_reflns_R_free 158 _refine.ls_number_parameters 1396 _refine.ls_number_restraints 1695 _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 '(PRO-HYP-GLY)10 structure reported in V.NAGARAJAN, S.KAMITORI, K.OKUYAMA, J.BIOCHEM.,125, 310 (1999).' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _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 ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_phase_error ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_analyze.entry_id 1V7H _refine_analyze.Luzzati_coordinate_error_obs ? _refine_analyze.Luzzati_sigma_a_obs ? _refine_analyze.Luzzati_d_res_low_obs ? _refine_analyze.Luzzati_coordinate_error_free ? _refine_analyze.Luzzati_sigma_a_free ? _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues 0 _refine_analyze.occupancy_sum_hydrogen 112.00 _refine_analyze.occupancy_sum_non_hydrogen 182.00 _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 133 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 49 _refine_hist.number_atoms_total 182 _refine_hist.d_res_high 1.25 _refine_hist.d_res_low 10.00 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function s_bond_d 0.016 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.026 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0368 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.106 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.029 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.006 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.031 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used ? _refine_ls_shell.d_res_high 1.25 _refine_ls_shell.d_res_low 1.30 _refine_ls_shell.number_reflns_R_work ? _refine_ls_shell.R_factor_R_work 0.126 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free ? _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free ? _refine_ls_shell.number_reflns_obs 315 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # _pdbx_refine.entry_id 1V7H _pdbx_refine.R_factor_all_no_cutoff 0.1653 _pdbx_refine.R_factor_obs_no_cutoff 0.1271 _pdbx_refine.free_R_factor_no_cutoff 0.2296 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 4.7 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 142 _pdbx_refine.R_factor_all_4sig_cutoff 0.1652 _pdbx_refine.R_factor_obs_4sig_cutoff 0.1271 _pdbx_refine.free_R_factor_4sig_cutoff 0.2296 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 4.7 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 142 _pdbx_refine.number_reflns_obs_4sig_cutoff 3015 _pdbx_refine.number_reflns_obs_no_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _database_PDB_matrix.entry_id 1V7H _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] 0.000000 _database_PDB_matrix.origx_vector[2] 0.000000 _database_PDB_matrix.origx_vector[3] 0.000000 # _struct.entry_id 1V7H _struct.title 'Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Sequence at 1.26 A' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1V7H _struct_keywords.pdbx_keywords 'STRUCTURAL PROTEIN' _struct_keywords.text 'Collagen, Triple-helix, Model peptide, STRUCTURAL PROTEIN' # 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 2 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 4 ? # loop_ _struct_ref.id _struct_ref.entity_id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 1 PDB 1V7H 1V7H ? ? ? 2 2 PDB 1V7H 1V7H ? ? ? 3 3 PDB 1V7H 1V7H ? ? ? # 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 1V7H A 1 ? 7 ? 1V7H 1 ? 7 ? 1 7 2 2 1V7H B 1 ? 7 ? 1V7H 1 ? 7 ? 1 7 3 3 1V7H C 1 ? 7 ? 1V7H 1 ? 7 ? 1 7 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 1_556 x,y,z+1 1.0000000000 0.0000000000 0.0000000000 -5.4833271118 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 19.1858082912 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ;THE ENTIRE 30 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 2 - 7 BY (001), AND RESIDUES 1-7 BY (002),(003),(004), AND RESIDUES 1-4 BY (005) CHAIN B: TRANSLATE RESIDUES 3 - 7 BY (001), AND RESIDUES 1-7 BY (002),(003),(004) AND RESIDUE 1-2 BY (005). CHAIN C: TRANSLATE RESIDUES 1 - 7 BY (001),(002),(003),(004), AND RESIDUES 1-3 BY (005). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 90 RESIDUES, 30 IN EACH CHAIN. ; # 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 _struct_conn.pdbx_role covale1 covale both ? A GLY 1 N ? ? ? 1_556 B HYP 7 C ? ? A GLY 1 B HYP 7 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale2 covale both ? A PRO 2 C ? ? ? 1_555 A HYP 3 N ? ? A PRO 2 A HYP 3 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale3 covale both ? A HYP 3 C ? ? ? 1_555 A GLY 4 N ? ? A HYP 3 A GLY 4 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale4 covale both ? A PRO 5 C ? ? ? 1_555 A HYP 6 N ? ? A PRO 5 A HYP 6 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale5 covale both ? A HYP 6 C ? ? ? 1_555 A GLY 7 N ? ? A HYP 6 A GLY 7 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale6 covale both ? B HYP 1 C ? ? ? 1_555 B GLY 2 N ? ? B HYP 1 B GLY 2 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale7 covale both ? B HYP 1 N ? ? ? 1_555 C PRO 7 C ? ? B HYP 1 C PRO 7 1_554 ? ? ? ? ? ? ? 1.329 ? ? covale8 covale both ? B PRO 3 C ? ? ? 1_555 B HYP 4 N ? ? B PRO 3 B HYP 4 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale9 covale both ? B HYP 4 C ? ? ? 1_555 B GLY 5 N ? ? B HYP 4 B GLY 5 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale10 covale both ? B PRO 6 C ? ? ? 1_555 B HYP 7 N ? ? B PRO 6 B HYP 7 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale11 covale both ? C PRO 1 C ? ? ? 1_555 C HYP 2 N ? ? C PRO 1 C HYP 2 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale12 covale both ? C HYP 2 C ? ? ? 1_555 C GLY 3 N ? ? C HYP 2 C GLY 3 1_555 ? ? ? ? ? ? ? 1.317 ? ? covale13 covale both ? C PRO 4 C ? ? ? 1_555 C HYP 5 N ? ? C PRO 4 C HYP 5 1_555 ? ? ? ? ? ? ? 1.350 ? ? covale14 covale both ? C HYP 5 C ? ? ? 1_555 C GLY 6 N ? ? C HYP 5 C GLY 6 1_555 ? ? ? ? ? ? ? 1.319 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 C _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 GLY _pdbx_validate_symm_contact.auth_seq_id_1 7 _pdbx_validate_symm_contact.PDB_ins_code_1 ? _pdbx_validate_symm_contact.label_alt_id_1 ? _pdbx_validate_symm_contact.site_symmetry_1 1_555 _pdbx_validate_symm_contact.auth_atom_id_2 N _pdbx_validate_symm_contact.auth_asym_id_2 C _pdbx_validate_symm_contact.auth_comp_id_2 PRO _pdbx_validate_symm_contact.auth_seq_id_2 1 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 1_556 _pdbx_validate_symm_contact.dist 1.32 # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A HYP 3 A HYP 3 ? PRO 4-HYDROXYPROLINE 2 A HYP 6 A HYP 6 ? PRO 4-HYDROXYPROLINE 3 B HYP 1 B HYP 1 ? PRO 4-HYDROXYPROLINE 4 B HYP 4 B HYP 4 ? PRO 4-HYDROXYPROLINE 5 B HYP 7 B HYP 7 ? PRO 4-HYDROXYPROLINE 6 C HYP 2 C HYP 2 ? PRO 4-HYDROXYPROLINE 7 C HYP 5 C HYP 5 ? PRO 4-HYDROXYPROLINE # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.pdbx_ordinal GLY N N N N 1 GLY CA C N N 2 GLY C C N N 3 GLY O O N N 4 GLY OXT O N N 5 GLY H H N N 6 GLY H2 H N N 7 GLY HA2 H N N 8 GLY HA3 H N N 9 GLY HXT H N N 10 HOH O O N N 11 HOH H1 H N N 12 HOH H2 H N N 13 HYP N N N N 14 HYP CA C N S 15 HYP C C N N 16 HYP O O N N 17 HYP CB C N N 18 HYP CG C N R 19 HYP CD C N N 20 HYP OD1 O N N 21 HYP OXT O N N 22 HYP H H N N 23 HYP HA H N N 24 HYP HB2 H N N 25 HYP HB3 H N N 26 HYP HG H N N 27 HYP HD22 H N N 28 HYP HD23 H N N 29 HYP HD1 H N N 30 HYP HXT H N N 31 PRO N N N N 32 PRO CA C N S 33 PRO C C N N 34 PRO O O N N 35 PRO CB C N N 36 PRO CG C N N 37 PRO CD C N N 38 PRO OXT O N N 39 PRO H H N N 40 PRO HA H N N 41 PRO HB2 H N N 42 PRO HB3 H N N 43 PRO HG2 H N N 44 PRO HG3 H N N 45 PRO HD2 H N N 46 PRO HD3 H N N 47 PRO HXT H N N 48 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.value_order _chem_comp_bond.pdbx_aromatic_flag _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_ordinal GLY N CA sing N N 1 GLY N H sing N N 2 GLY N H2 sing N N 3 GLY CA C sing N N 4 GLY CA HA2 sing N N 5 GLY CA HA3 sing N N 6 GLY C O doub N N 7 GLY C OXT sing N N 8 GLY OXT HXT sing N N 9 HOH O H1 sing N N 10 HOH O H2 sing N N 11 HYP N CA sing N N 12 HYP N CD sing N N 13 HYP N H sing N N 14 HYP CA C sing N N 15 HYP CA CB sing N N 16 HYP CA HA sing N N 17 HYP C O doub N N 18 HYP C OXT sing N N 19 HYP CB CG sing N N 20 HYP CB HB2 sing N N 21 HYP CB HB3 sing N N 22 HYP CG CD sing N N 23 HYP CG OD1 sing N N 24 HYP CG HG sing N N 25 HYP CD HD22 sing N N 26 HYP CD HD23 sing N N 27 HYP OD1 HD1 sing N N 28 HYP OXT HXT sing N N 29 PRO N CA sing N N 30 PRO N CD sing N N 31 PRO N H sing N N 32 PRO CA C sing N N 33 PRO CA CB sing N N 34 PRO CA HA sing N N 35 PRO C O doub N N 36 PRO C OXT sing N N 37 PRO CB CG sing N N 38 PRO CB HB2 sing N N 39 PRO CB HB3 sing N N 40 PRO CG CD sing N N 41 PRO CG HG2 sing N N 42 PRO CG HG3 sing N N 43 PRO CD HD2 sing N N 44 PRO CD HD3 sing N N 45 PRO OXT HXT sing N N 46 # _pdbx_initial_refinement_model.accession_code ? _pdbx_initial_refinement_model.id 1 _pdbx_initial_refinement_model.entity_id_list ? _pdbx_initial_refinement_model.type 'experimental model' _pdbx_initial_refinement_model.source_name Other _pdbx_initial_refinement_model.details '(PRO-HYP-GLY)10 structure reported in V.NAGARAJAN, S.KAMITORI, K.OKUYAMA, J.BIOCHEM.,125, 310 (1999).' # _atom_sites.entry_id 1V7H _atom_sites.fract_transf_matrix[1][1] 0.071983 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.020578 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.038292 _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] 0.052123 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O # loop_