data_1V6Q # _entry.id 1V6Q # _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 1V6Q pdb_00001v6q 10.2210/pdb1v6q/pdb RCSB RCSB006275 ? ? WWPDB D_1000006275 ? ? # 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 1V6Q _pdbx_database_status.recvd_initial_deposition_date 2003-12-03 _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 peptide measured at 100K' unspecified PDB 1V7H 'holomologous peptide measured at 100K' 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 42 ? ? ? ? # 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 1 103 103 GLY GLY A . n A 1 2 PRO 2 104 104 PRO PRO A . n A 1 3 HYP 3 105 105 HYP HYP A . n A 1 4 GLY 4 106 106 GLY GLY A . n A 1 5 PRO 5 107 107 PRO PRO A . n A 1 6 HYP 6 108 108 HYP HYP A . n A 1 7 GLY 7 109 109 GLY GLY A . n B 2 1 HYP 1 202 202 HYP HYP B . n B 2 2 GLY 2 203 203 GLY GLY B . n B 2 3 PRO 3 204 204 PRO PRO B . n B 2 4 HYP 4 205 205 HYP HYP B . n B 2 5 GLY 5 206 206 GLY GLY B . n B 2 6 PRO 6 207 207 PRO PRO B . n B 2 7 HYP 7 208 208 HYP HYP B . n C 3 1 PRO 1 301 301 PRO PRO C . n C 3 2 HYP 2 302 302 HYP HYP C . n C 3 3 GLY 3 303 303 GLY GLY C . n C 3 4 PRO 4 304 304 PRO PRO C . n C 3 5 HYP 5 305 305 HYP HYP C . n C 3 6 GLY 6 306 306 GLY GLY C . n C 3 7 PRO 7 307 307 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 1 401 401 HOH HOH A . D 4 HOH 2 402 402 HOH HOH A . D 4 HOH 3 403 403 HOH HOH A . D 4 HOH 4 404 404 HOH HOH A . D 4 HOH 5 405 405 HOH HOH A . D 4 HOH 6 406 406 HOH HOH A . D 4 HOH 7 407 407 HOH HOH A . D 4 HOH 8 409 409 HOH HOH A . D 4 HOH 9 428 428 HOH HOH A . D 4 HOH 10 430 430 HOH HOH A . D 4 HOH 11 438 438 HOH HOH A . D 4 HOH 12 439 439 HOH HOH A . D 4 HOH 13 447 447 HOH HOH A . D 4 HOH 14 449 449 HOH HOH A . E 4 HOH 1 410 410 HOH HOH B . E 4 HOH 2 412 412 HOH HOH B . E 4 HOH 3 413 413 HOH HOH B . E 4 HOH 4 414 414 HOH HOH B . E 4 HOH 5 415 415 HOH HOH B . E 4 HOH 6 416 416 HOH HOH B . E 4 HOH 7 418 418 HOH HOH B . E 4 HOH 8 419 419 HOH HOH B . E 4 HOH 9 420 420 HOH HOH B . E 4 HOH 10 421 421 HOH HOH B . E 4 HOH 11 433 433 HOH HOH B . E 4 HOH 12 434 434 HOH HOH B . E 4 HOH 13 445 445 HOH HOH B . E 4 HOH 14 448 448 HOH HOH B . E 4 HOH 15 506 506 HOH HOH B . F 4 HOH 1 408 408 HOH HOH C . F 4 HOH 2 411 411 HOH HOH C . F 4 HOH 3 417 417 HOH HOH C . F 4 HOH 4 422 422 HOH HOH C . F 4 HOH 5 423 423 HOH HOH C . F 4 HOH 6 424 424 HOH HOH C . F 4 HOH 7 425 425 HOH HOH C . F 4 HOH 8 426 426 HOH HOH C . F 4 HOH 9 427 427 HOH HOH C . F 4 HOH 10 429 429 HOH HOH C . F 4 HOH 11 432 432 HOH HOH C . F 4 HOH 12 435 435 HOH HOH C . F 4 HOH 13 443 443 HOH HOH C . # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal CrystalClear 'data collection' . ? 1 CrystalClear 'data reduction' . ? 2 SHELX 'model building' . ? 3 SHELXL-97 refinement . ? 4 CrystalClear 'data scaling' . ? 5 SHELX phasing . ? 6 # _cell.entry_id 1V6Q _cell.length_a 14.051 _cell.length_b 26.775 _cell.length_c 20.004 _cell.angle_alpha 90.00 _cell.angle_beta 106.76 _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 1V6Q _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 1V6Q _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 34.28 _exptl_crystal.description ? _exptl_crystal.density_Matthews 1.87 _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 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details 'PEG 200, Acetic acid, Sodium azide, VAPOR DIFFUSION, HANGING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 293 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 4' _diffrn_detector.pdbx_collection_date 2002-06-25 _diffrn_detector.details '1-M-LONG BENT-CYLINDER MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'FIXED-EXIT DOUBLE CRYSTAL' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.00 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'SPRING-8 BEAMLINE BL40B2' _diffrn_source.pdbx_synchrotron_site SPring-8 _diffrn_source.pdbx_synchrotron_beamline BL40B2 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.00 # _reflns.entry_id 1V6Q _reflns.observed_criterion_sigma_I 1.0 _reflns.observed_criterion_sigma_F 1.0 _reflns.d_resolution_low 19.15 _reflns.d_resolution_high 1.25 _reflns.number_obs 3768 _reflns.number_all ? _reflns.percent_possible_obs 94.5 _reflns.pdbx_Rmerge_I_obs 0.057 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 7.6 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 3.4 _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 1.25 _reflns_shell.d_res_low 1.30 _reflns_shell.percent_possible_all 67.7 _reflns_shell.Rmerge_I_obs 0.235 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 2.4 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 268 _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 1V6Q _refine.ls_number_reflns_obs 3547 _refine.ls_number_reflns_all 3733 _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 89.1 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.1346 _refine.ls_R_factor_R_free 0.1886 _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 186 _refine.ls_number_parameters 1368 _refine.ls_number_restraints 1698 _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 ;The polymer structure can be generated from the submitted asymmetric unit by applying the (0 0 1) translation using fractional coordinates. ; _refine.pdbx_starting_model '(Pro-Hyp-Gly)10 structure reported in V.Nagarajan, S.Kamitori and 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_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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 1V6Q _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 175.00 _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 42 _refine_hist.number_atoms_total 175 _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 0.018 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d 0.023 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist 0.000 ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes 0.0314 ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol 0.093 ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol 0.033 ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr 0.014 ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt 0.005 ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt 0.037 ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps 0.000 ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1V6Q _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff 0.1346 _pdbx_refine.free_R_factor_no_cutoff 0.1886 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff 5.0 _pdbx_refine.free_R_val_test_set_ct_no_cutoff 186 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff 0.1273 _pdbx_refine.free_R_factor_4sig_cutoff 0.1797 _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff 5.0 _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff 157 _pdbx_refine.number_reflns_obs_4sig_cutoff 3142 _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 1V6Q _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 1V6Q _struct.title 'Crystal Structures of Collagen Model Peptides with Pro-Hyp-Gly Sequence at 1.3 A' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1V6Q _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 1V6Q 1V6Q ? ? ? 2 2 PDB 1V6Q 1V6Q ? ? ? 3 3 PDB 1V6Q 1V6Q ? ? ? # 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 1V6Q A 1 ? 7 ? 1V6Q 103 ? 109 ? 103 109 2 2 1V6Q B 1 ? 7 ? 1V6Q 202 ? 208 ? 202 208 3 3 1V6Q C 1 ? 7 ? 1V6Q 301 ? 307 ? 301 307 # _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 -5.7684212831 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 19.1542510138 # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ;THE ENTIRE 33 RESIDUE LONG PEPTIDE CAN BE GENERATED FROM THE SUBMITTED ASYMMETRIC UNIT BY APPLYING THE FOLLOWING TRANSLATIONS (USING FRACTIONAL COORDINATES): CHAIN A: TRANSLATE RESIDUES 104-109 BY (001), AND RESIDUES 103-109 BY (002), (003), (004)(005). CHAIN B: TRANSLATE RESIDUES 204 - 208 BY (001), AND RESIDUES 202-208 BY (002), (003), (004) AND RESIDUE 202-206 BY (005). CHAIN C: TRANSLATE RESIDUES 301 - 307 BY (001), (002), (003) (004), AND RESIDUES 301-306 BY (005). THIS WILL RESULT IN A MOLECULE WITH A TOTAL OF 99 RESIDUES, 33 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 103 B HYP 208 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale2 covale both ? A PRO 2 C ? ? ? 1_555 A HYP 3 N ? ? A PRO 104 A HYP 105 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale3 covale both ? A HYP 3 C ? ? ? 1_555 A GLY 4 N ? ? A HYP 105 A GLY 106 1_555 ? ? ? ? ? ? ? 1.316 ? ? covale4 covale both ? A PRO 5 C ? ? ? 1_555 A HYP 6 N ? ? A PRO 107 A HYP 108 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale5 covale both ? A HYP 6 C ? ? ? 1_555 A GLY 7 N ? ? A HYP 108 A GLY 109 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale6 covale both ? B HYP 1 C ? ? ? 1_555 B GLY 2 N ? ? B HYP 202 B GLY 203 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale7 covale both ? B HYP 1 N ? ? ? 1_555 C PRO 7 C ? ? B HYP 202 C PRO 307 1_554 ? ? ? ? ? ? ? 1.333 ? ? covale8 covale both ? B PRO 3 C ? ? ? 1_555 B HYP 4 N ? ? B PRO 204 B HYP 205 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale9 covale both ? B HYP 4 C ? ? ? 1_555 B GLY 5 N ? ? B HYP 205 B GLY 206 1_555 ? ? ? ? ? ? ? 1.317 ? ? covale10 covale both ? B PRO 6 C ? ? ? 1_555 B HYP 7 N ? ? B PRO 207 B HYP 208 1_555 ? ? ? ? ? ? ? 1.323 ? ? covale11 covale both ? C PRO 1 C ? ? ? 1_555 C HYP 2 N ? ? C PRO 301 C HYP 302 1_555 ? ? ? ? ? ? ? 1.322 ? ? covale12 covale both ? C HYP 2 C ? ? ? 1_555 C GLY 3 N ? ? C HYP 302 C GLY 303 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale13 covale both ? C PRO 4 C ? ? ? 1_555 C HYP 5 N ? ? C PRO 304 C HYP 305 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale14 covale both ? C HYP 5 C ? ? ? 1_555 C GLY 6 N ? ? C HYP 305 C GLY 306 1_555 ? ? ? ? ? ? ? 1.315 ? ? # _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_1 109 _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_2 301 _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 1.34 # 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 105 ? PRO 4-HYDROXYPROLINE 2 A HYP 6 A HYP 108 ? PRO 4-HYDROXYPROLINE 3 B HYP 1 B HYP 202 ? PRO 4-HYDROXYPROLINE 4 B HYP 4 B HYP 205 ? PRO 4-HYDROXYPROLINE 5 B HYP 7 B HYP 208 ? PRO 4-HYDROXYPROLINE 6 C HYP 2 C HYP 302 ? PRO 4-HYDROXYPROLINE 7 C HYP 5 C HYP 305 ? 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 and K.Okuyama, J.Biochem., 125, 310 (1999).' # _atom_sites.entry_id 1V6Q _atom_sites.fract_transf_matrix[1][1] 0.071169 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.021433 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.037348 _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] 0.052208 _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_