data_1COQ # _entry.id 1COQ # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.280 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1COQ WWPDB D_1000172438 # _pdbx_database_PDB_obs_spr.id OBSLTE _pdbx_database_PDB_obs_spr.date 1999-09-24 _pdbx_database_PDB_obs_spr.pdb_id NONE _pdbx_database_PDB_obs_spr.replace_pdb_id 1COQ _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_status.status_code OBS _pdbx_database_status.entry_id 1COQ _pdbx_database_status.recvd_initial_deposition_date 1999-07-20 _pdbx_database_status.deposit_site BNL _pdbx_database_status.process_site BNL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Loll, P.J.' 1 'Kaplan, J.' 2 'Selinsky, B.' 3 'Axelsen, P.H.' 4 # _citation.id primary _citation.title 'Vancomycin Binding to Low Affinity Ligands: Delineating a Minimum Set of Interactions Necessary for High Affinity Binding' _citation.journal_abbrev 'To be Published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Loll, P.J.' 1 primary 'Kaplan, J.' 2 primary 'Selinsky, B.' 3 primary 'Axelsen, P.H.' 4 # _cell.entry_id 1COQ _cell.length_a 28.400 _cell.length_b 28.400 _cell.length_c 65.730 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1COQ _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 # 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 non-polymer syn 'CHLORIDE ION' 35.453 3 ? ? ? ? 2 non-polymer syn VANCOMYCIN 1451.269 2 ? ? ? ? 3 non-polymer syn 'LACTIC ACID' 90.078 1 ? ? ? ? 4 water nat water 18.015 45 ? ? ? ? # 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 CL non-polymer . 'CHLORIDE ION' ? 'Cl -1' 35.453 HOH non-polymer . WATER ? 'H2 O' 18.015 LAC non-polymer . 'LACTIC ACID' ? 'C3 H6 O3' 90.078 VAN non-polymer . VANCOMYCIN ? 'C66 H77 Cl2 N9 O24 2' 1451.269 # _exptl.entry_id 1COQ _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _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 4.60 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details 'pH 4.60' # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector 'IMAGE PLATE' _diffrn_detector.type 'MAR 30 CM' _diffrn_detector.pdbx_collection_date 1997-05-05 _diffrn_detector.details ? # _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 0.978 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS X12B' _diffrn_source.pdbx_synchrotron_site 'NSLS X12B' _diffrn_source.pdbx_synchrotron_beamline ? _diffrn_source.pdbx_wavelength 0.978 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 1COQ _reflns.observed_criterion_sigma_I 2.000 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 20.000 _reflns.d_resolution_high 1.000 _reflns.number_obs 13845 _reflns.number_all ? _reflns.percent_possible_obs 92.0 _reflns.pdbx_Rmerge_I_obs 0.054 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI 34.7000 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 11.800 _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.pdbx_netI_over_sigmaI ? # _reflns_shell.d_res_high 1.00 _reflns_shell.d_res_low 1.04 _reflns_shell.percent_possible_all 65.0 _reflns_shell.Rmerge_I_obs 0.055 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs ? _reflns_shell.pdbx_redundancy 2.40 _reflns_shell.pdbx_diffrn_id ? _reflns_shell.pdbx_ordinal 1 # _refine.entry_id 1COQ _refine.ls_number_reflns_obs ? _refine.ls_number_reflns_all 15091 _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 1.00 _refine.ls_percent_reflns_obs 92.0 _refine.ls_R_factor_obs ? _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free 0.139 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free 1002 _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 ? _refine.details ;REFINEMENT WAS CARRIED OUT AGAINST F-SQUARED USING SHELXL-93.MOLECULAR GEOMETRY AND ATOMIC DISPLACEMENT PARAMETERS WERE RESTRAINED THROUGHOUT. INDEPENDENT VANCOMYCIN MONOMERS WERE RESTRAINED TO HAVE SIMILAR 1-2 AND 1-3 DISTANCES; RESTRAINTS WERE ALSO IMPOSED TO LIMIT DEVIATIONS FROM PLANARITY IN RINGS AND SP2 SYSTEMS.ALONG-BOND COMPONENTS OF ANISOTROPIC DISPLACEMENT PARAMETERS WERE SUBJECTED TO RESTRAINTS. SOLVENT WATER ATOMS WERE RESTRAINED TO BE APPROXIMATELY ISOTROPIC AND WERE MADE SUBJECT TO ANTI- BUMPING RESTRAINTS. CONJUGATE GRADIENT REFINEMENT WAS USED THROUGHOUT, EXCEPT AT THE LAST STAGES, WHEN BLOCKED LEAST SQUARES WAS USED. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _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 ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 223 _refine_hist.number_atoms_solvent 46 _refine_hist.number_atoms_total 269 _refine_hist.d_res_high 1.00 _refine_hist.d_res_low 20.0 _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' # 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 0.019 ? ? ? 'X-RAY DIFFRACTION' ? s_angle_d ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_dist ? ? ? ? 'X-RAY DIFFRACTION' ? s_from_restr_planes ? ? ? ? 'X-RAY DIFFRACTION' ? s_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_non_zero_chiral_vol ? ? ? ? 'X-RAY DIFFRACTION' ? s_anti_bump_dis_restr ? ? ? ? 'X-RAY DIFFRACTION' ? s_rigid_bond_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_similar_adp_cmpnt ? ? ? ? 'X-RAY DIFFRACTION' ? s_approx_iso_adps ? ? ? ? 'X-RAY DIFFRACTION' ? # _pdbx_refine.entry_id 1COQ _pdbx_refine.R_factor_all_no_cutoff ? _pdbx_refine.R_factor_obs_no_cutoff ? _pdbx_refine.free_R_factor_no_cutoff 0.139 _pdbx_refine.free_R_val_test_set_size_perc_no_cutoff ? _pdbx_refine.free_R_val_test_set_ct_no_cutoff 1002 _pdbx_refine.R_factor_all_4sig_cutoff ? _pdbx_refine.R_factor_obs_4sig_cutoff ? _pdbx_refine.free_R_factor_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_size_perc_4sig_cutoff ? _pdbx_refine.free_R_val_test_set_ct_4sig_cutoff ? _pdbx_refine.number_reflns_obs_4sig_cutoff ? _pdbx_refine.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine.free_R_error_no_cutoff ? # _struct.entry_id 1COQ _struct.title 'COMPLEX OF VANCOMYCIN WITH 2-ACETOXY-D-PROPANOIC ACID' _struct.pdbx_descriptor 'INHIBITOR, VANCOMYCIN, LACTIC ACID' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1COQ _struct_keywords.pdbx_keywords INHIBITOR _struct_keywords.text 'GLYCOPEPTIDE ANTIBIOTIC, INHIBITOR' # 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 1 ? D N N 2 ? E N N 2 ? F N N 3 ? G N N 4 ? # _struct_biol.id 1 # _database_PDB_matrix.entry_id 1COQ _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 1COQ _atom_sites.fract_transf_matrix[1][1] 0.035211 _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] 0.035211 _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] 0.015214 _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 CL N O # 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 A 1 CL 1 3 3 CL CL ? . B 1 CL 1 4 4 CL CL ? . C 1 CL 1 5 5 CL CL ? . D 2 VAN 1 1 1 VAN VAN ? . E 2 VAN 1 2 2 VAN VAN ? . F 3 LAC 1 6 6 LAC LAC ? . G 4 HOH 1 10 10 HOH HOH ? . G 4 HOH 2 11 11 HOH HOH ? . G 4 HOH 3 12 12 HOH HOH ? . G 4 HOH 4 13 13 HOH HOH ? . G 4 HOH 5 14 14 HOH HOH ? . G 4 HOH 6 15 15 HOH HOH ? . G 4 HOH 7 16 16 HOH HOH ? . G 4 HOH 8 17 17 HOH HOH ? . G 4 HOH 9 18 18 HOH HOH ? . G 4 HOH 10 19 19 HOH HOH ? . G 4 HOH 11 20 20 HOH HOH ? . G 4 HOH 12 21 21 HOH HOH ? . G 4 HOH 13 22 22 HOH HOH ? . G 4 HOH 14 23 23 HOH HOH ? . G 4 HOH 15 24 24 HOH HOH ? . G 4 HOH 16 25 25 HOH HOH ? . G 4 HOH 17 26 26 HOH HOH ? . G 4 HOH 18 27 27 HOH HOH ? . G 4 HOH 19 28 28 HOH HOH ? . G 4 HOH 20 29 29 HOH HOH ? . G 4 HOH 21 30 30 HOH HOH ? . G 4 HOH 22 31 31 HOH HOH ? . G 4 HOH 23 32 32 HOH HOH ? . G 4 HOH 24 33 33 HOH HOH ? . G 4 HOH 25 34 34 HOH HOH ? . G 4 HOH 26 35 35 HOH HOH ? . G 4 HOH 27 36 36 HOH HOH ? . G 4 HOH 28 37 37 HOH HOH ? . G 4 HOH 29 38 38 HOH HOH ? . G 4 HOH 30 39 39 HOH HOH ? . G 4 HOH 31 40 40 HOH HOH ? . G 4 HOH 32 41 41 HOH HOH ? . G 4 HOH 33 42 42 HOH HOH ? . G 4 HOH 34 43 43 HOH HOH ? . G 4 HOH 35 44 44 HOH HOH ? . G 4 HOH 36 45 45 HOH HOH ? . G 4 HOH 37 51 51 HOH HOH ? . G 4 HOH 38 52 52 HOH HOH ? . G 4 HOH 39 53 53 HOH HOH ? . G 4 HOH 40 54 54 HOH HOH ? . G 4 HOH 41 55 55 HOH HOH ? . G 4 HOH 42 56 56 HOH HOH ? . G 4 HOH 43 57 57 HOH HOH ? . G 4 HOH 44 58 58 HOH HOH ? . G 4 HOH 45 59 59 HOH HOH ? . # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id . _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 44 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id G _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # 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 1999-07-30 2 'Structure model' 1 1 1999-09-24 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description 1 1 'Structure model' repository 'Initial release' ? 2 2 'Structure model' repository Obsolete ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal DENZO 'data collection' . ? 1 SCALEPACK 'data reduction' . ? 2 SHELXL-93 'model building' . ? 3 SHELXL-93 refinement . ? 4 DENZO 'data reduction' . ? 5 SCALEPACK 'data scaling' . ? 6 SHELXL-93 phasing . ? 7 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 1 'CHLORIDE ION' CL 2 VANCOMYCIN VAN 3 'LACTIC ACID' LAC 4 water HOH #