data_3NVF # _entry.id 3NVF # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.387 _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 3NVF pdb_00003nvf 10.2210/pdb3nvf/pdb RCSB RCSB060327 ? ? WWPDB D_1000060327 ? ? # 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 2011-03-02 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2024-02-21 # _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' 'Data collection' 3 3 'Structure model' 'Database references' 4 3 'Structure model' 'Derived calculations' # 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 3 'Structure model' chem_comp_atom 2 3 'Structure model' chem_comp_bond 3 3 'Structure model' database_2 4 3 'Structure model' struct_site # 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 3 'Structure model' '_database_2.pdbx_DOI' 2 3 'Structure model' '_database_2.pdbx_database_accession' 3 3 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 3 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 3 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_database_status.entry_id 3NVF _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-07-08 _pdbx_database_status.status_code_sf REL _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3NVE 'MMHFGN hexapeptide (residues 138-143) from golden hamster prion protein' unspecified PDB 3NVG 'MIHFGN hexapeptide (residues 137-142) from mouse prion protein' unspecified PDB 3NVH 'MIHFGND (residues 137-143) from mouse prion protein' unspecified # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Apostol, M.I.' 1 'Sawaya, M.R.' 2 'Eisenberg, D.' 3 # _citation.id primary _citation.title 'Atomic structures suggest determinants of transmission barriers in Mammalian prion disease.' _citation.journal_abbrev Biochemistry _citation.journal_volume 50 _citation.page_first 2456 _citation.page_last 2463 _citation.year 2011 _citation.journal_id_ASTM BICHAW _citation.country US _citation.journal_id_ISSN 0006-2960 _citation.journal_id_CSD 0033 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 21323366 _citation.pdbx_database_id_DOI 10.1021/bi101803k # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Apostol, M.I.' 1 ? primary 'Wiltzius, J.J.' 2 ? primary 'Sawaya, M.R.' 3 ? primary 'Cascio, D.' 4 ? primary 'Eisenberg, D.' 5 ? # 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 'Major prion protein' 673.781 1 ? ? ? ? 2 non-polymer syn '(4S)-2-METHYL-2,4-PENTANEDIOL' 118.174 1 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'PrP, PrP27-30, PrP33-35C, ASCR' # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code IIHFGS _entity_poly.pdbx_seq_one_letter_code_can IIHFGS _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name '(4S)-2-METHYL-2,4-PENTANEDIOL' _pdbx_entity_nonpoly.comp_id MPD # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ILE n 1 2 ILE n 1 3 HIS n 1 4 PHE n 1 5 GLY n 1 6 SER n # _pdbx_entity_src_syn.entity_id 1 _pdbx_entity_src_syn.pdbx_src_id 1 _pdbx_entity_src_syn.pdbx_alt_source_flag sample _pdbx_entity_src_syn.pdbx_beg_seq_num ? _pdbx_entity_src_syn.pdbx_end_seq_num ? _pdbx_entity_src_syn.organism_scientific 'Homo sapiens' _pdbx_entity_src_syn.organism_common_name human _pdbx_entity_src_syn.ncbi_taxonomy_id 9606 _pdbx_entity_src_syn.details 'IIHFGS (UNP residues 138-143) from human prion' # 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 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 MPD non-polymer . '(4S)-2-METHYL-2,4-PENTANEDIOL' ? 'C6 H14 O2' 118.174 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 # 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 ILE 1 1 1 ILE ILE A . n A 1 2 ILE 2 2 2 ILE ILE A . n A 1 3 HIS 3 3 3 HIS HIS A . n A 1 4 PHE 4 4 4 PHE PHE A . n A 1 5 GLY 5 5 5 GLY GLY A . n A 1 6 SER 6 6 6 SER SER A . n # _pdbx_nonpoly_scheme.asym_id B _pdbx_nonpoly_scheme.entity_id 2 _pdbx_nonpoly_scheme.mon_id MPD _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 7 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id MPD _pdbx_nonpoly_scheme.auth_mon_id MPD _pdbx_nonpoly_scheme.pdb_strand_id A _pdbx_nonpoly_scheme.pdb_ins_code . # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 PHASER 1.3.2 'Wed Feb 15 11:59:26 2006' program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 4 REFMAC . ? program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 5 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? # _cell.length_a 27.546 _cell.length_b 31.017 _cell.length_c 4.804 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3NVF _cell.pdbx_unique_axis ? _cell.Z_PDB 4 _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.space_group_name_H-M 'P 21 21 2' _symmetry.entry_id 3NVF _symmetry.Int_Tables_number 18 _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # _exptl.crystals_number 1 _exptl.entry_id 3NVF _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.52 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 19.23 _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.pH 7.4 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details '100mM Tris pH 7.4, 25% MPD, vapor diffusion, hanging drop, temperature 298K' _exptl_crystal_grow.temp_details ? _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 'MAR CCD 225' _diffrn_detector.pdbx_collection_date 2008-01-01 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.8726 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID13' _diffrn_source.pdbx_wavelength_list 0.8726 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID13 # _reflns.entry_id 3NVF _reflns.d_resolution_high 1.800 _reflns.d_resolution_low 90.000 _reflns.number_obs 443 _reflns.pdbx_Rmerge_I_obs 0.216 _reflns.pdbx_netI_over_sigmaI 6.800 _reflns.pdbx_chi_squared 1.137 _reflns.pdbx_redundancy 3.800 _reflns.percent_possible_obs 85.400 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _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_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 1.800 1.940 ? ? ? 0.395 ? ? 1.424 1.700 ? 63 67.000 ? 1 1.940 2.130 ? ? ? 0.327 ? ? 1.294 2.300 ? 83 85.600 ? 2 2.130 2.440 ? ? ? 0.314 ? ? 0.964 3.200 ? 89 78.800 ? 3 2.440 3.080 ? ? ? 0.244 ? ? 1.062 5.400 ? 87 100.000 ? 4 3.080 90.000 ? ? ? 0.197 ? ? 1.199 5.100 ? 121 94.500 ? 5 # _refine.entry_id 3NVF _refine.ls_d_res_high 1.8000 _refine.ls_d_res_low 20.6000 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 86.4300 _refine.ls_number_reflns_obs 433 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.2133 _refine.ls_R_factor_R_work 0.2118 _refine.ls_wR_factor_R_work 0.2013 _refine.ls_R_factor_R_free 0.2263 _refine.ls_wR_factor_R_free 0.2521 _refine.ls_percent_reflns_R_free 9.2000 _refine.ls_number_reflns_R_free 40 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 20.8202 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.0000 _refine.aniso_B[2][2] -0.0400 _refine.aniso_B[3][3] -0.9500 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9550 _refine.correlation_coeff_Fo_to_Fc_free 0.9400 _refine.overall_SU_R_Cruickshank_DPI 0.2379 _refine.overall_SU_R_free 0.1668 _refine.pdbx_overall_ESU_R_Free 0.1670 _refine.overall_SU_ML 0.1110 _refine.overall_SU_B 4.0090 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.4000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.8682 _refine.B_iso_max 52.980 _refine.B_iso_min 10.200 _refine.occupancy_max 1.000 _refine.occupancy_min 1.000 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _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_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 48 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 0 _refine_hist.number_atoms_total 56 _refine_hist.d_res_high 1.8000 _refine_hist.d_res_low 20.6000 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 56 0.009 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 35 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 75 1.657 2.043 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 84 0.693 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5 9.100 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 2 52.201 20.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 7 10.817 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 8 0.053 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 52 0.004 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 12 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 29 0.523 1.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 12 0.157 1.500 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 46 0.853 2.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 27 1.220 3.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 29 1.673 4.500 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.8000 _refine_ls_shell.d_res_low 2.0110 _refine_ls_shell.pdbx_total_number_of_bins_used 5 _refine_ls_shell.percent_reflns_obs 72.2200 _refine_ls_shell.number_reflns_R_work 87 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.3820 _refine_ls_shell.R_factor_R_free 0.3300 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 4 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 91 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3NVF _struct.title 'IIHFGS segment 138-143 from human prion' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3NVF _struct_keywords.text 'amyloid-like protofibril, PROTEIN FIBRIL' _struct_keywords.pdbx_keywords 'PROTEIN FIBRIL' # 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 ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PRIO_HUMAN _struct_ref.pdbx_db_accession P04156 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code IIHFGS _struct_ref.pdbx_align_begin 138 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3NVF _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 6 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession P04156 _struct_ref_seq.db_align_beg 138 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 143 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1 _struct_ref_seq.pdbx_auth_seq_align_end 6 # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details decameric _pdbx_struct_assembly.oligomeric_count 10 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8,9,10 _pdbx_struct_assembly_gen.asym_id_list A,B # 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_557 x,y,z+2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 9.6080000000 3 'crystal symmetry operation' 1_556 x,y,z+1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4.8040000000 4 'crystal symmetry operation' 1_554 x,y,z-1 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -4.8040000000 5 'crystal symmetry operation' 1_553 x,y,z-2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -9.6080000000 6 'crystal symmetry operation' 2_657 -x+1,-y,z+2 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 9.6080000000 7 'crystal symmetry operation' 2_656 -x+1,-y,z+1 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 4.8040000000 8 'crystal symmetry operation' 2_655 -x+1,-y,z -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 9 'crystal symmetry operation' 2_654 -x+1,-y,z-1 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -4.8040000000 10 'crystal symmetry operation' 2_653 -x+1,-y,z-2 -1.0000000000 0.0000000000 0.0000000000 27.5460000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 -9.6080000000 # _struct_biol.id 1 _struct_biol.details ? # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id MPD _struct_site.pdbx_auth_seq_id 7 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE MPD A 7' # 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 5 ILE A 1 ? ILE A 1 . ? 4_444 ? 2 AC1 5 ILE A 2 ? ILE A 2 . ? 4_444 ? 3 AC1 5 HIS A 3 ? HIS A 3 . ? 1_555 ? 4 AC1 5 HIS A 3 ? HIS A 3 . ? 1_554 ? 5 AC1 5 PHE A 4 ? PHE A 4 . ? 3_544 ? # _pdbx_phasing_MR.entry_id 3NVF _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor ? _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 2.200 _pdbx_phasing_MR.d_res_low_rotation 20.600 _pdbx_phasing_MR.d_res_high_translation 2.200 _pdbx_phasing_MR.d_res_low_translation 20.600 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # 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 HIS N N N N 11 HIS CA C N S 12 HIS C C N N 13 HIS O O N N 14 HIS CB C N N 15 HIS CG C Y N 16 HIS ND1 N Y N 17 HIS CD2 C Y N 18 HIS CE1 C Y N 19 HIS NE2 N Y N 20 HIS OXT O N N 21 HIS H H N N 22 HIS H2 H N N 23 HIS HA H N N 24 HIS HB2 H N N 25 HIS HB3 H N N 26 HIS HD1 H N N 27 HIS HD2 H N N 28 HIS HE1 H N N 29 HIS HE2 H N N 30 HIS HXT H N N 31 ILE N N N N 32 ILE CA C N S 33 ILE C C N N 34 ILE O O N N 35 ILE CB C N S 36 ILE CG1 C N N 37 ILE CG2 C N N 38 ILE CD1 C N N 39 ILE OXT O N N 40 ILE H H N N 41 ILE H2 H N N 42 ILE HA H N N 43 ILE HB H N N 44 ILE HG12 H N N 45 ILE HG13 H N N 46 ILE HG21 H N N 47 ILE HG22 H N N 48 ILE HG23 H N N 49 ILE HD11 H N N 50 ILE HD12 H N N 51 ILE HD13 H N N 52 ILE HXT H N N 53 MPD C1 C N N 54 MPD C2 C N N 55 MPD O2 O N N 56 MPD CM C N N 57 MPD C3 C N N 58 MPD C4 C N S 59 MPD O4 O N N 60 MPD C5 C N N 61 MPD H11 H N N 62 MPD H12 H N N 63 MPD H13 H N N 64 MPD HO2 H N N 65 MPD HM1 H N N 66 MPD HM2 H N N 67 MPD HM3 H N N 68 MPD H31 H N N 69 MPD H32 H N N 70 MPD H4 H N N 71 MPD HO4 H N N 72 MPD H51 H N N 73 MPD H52 H N N 74 MPD H53 H N N 75 PHE N N N N 76 PHE CA C N S 77 PHE C C N N 78 PHE O O N N 79 PHE CB C N N 80 PHE CG C Y N 81 PHE CD1 C Y N 82 PHE CD2 C Y N 83 PHE CE1 C Y N 84 PHE CE2 C Y N 85 PHE CZ C Y N 86 PHE OXT O N N 87 PHE H H N N 88 PHE H2 H N N 89 PHE HA H N N 90 PHE HB2 H N N 91 PHE HB3 H N N 92 PHE HD1 H N N 93 PHE HD2 H N N 94 PHE HE1 H N N 95 PHE HE2 H N N 96 PHE HZ H N N 97 PHE HXT H N N 98 SER N N N N 99 SER CA C N S 100 SER C C N N 101 SER O O N N 102 SER CB C N N 103 SER OG O N N 104 SER OXT O N N 105 SER H H N N 106 SER H2 H N N 107 SER HA H N N 108 SER HB2 H N N 109 SER HB3 H N N 110 SER HG H N N 111 SER HXT H N N 112 # 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 HIS N CA sing N N 10 HIS N H sing N N 11 HIS N H2 sing N N 12 HIS CA C sing N N 13 HIS CA CB sing N N 14 HIS CA HA sing N N 15 HIS C O doub N N 16 HIS C OXT sing N N 17 HIS CB CG sing N N 18 HIS CB HB2 sing N N 19 HIS CB HB3 sing N N 20 HIS CG ND1 sing Y N 21 HIS CG CD2 doub Y N 22 HIS ND1 CE1 doub Y N 23 HIS ND1 HD1 sing N N 24 HIS CD2 NE2 sing Y N 25 HIS CD2 HD2 sing N N 26 HIS CE1 NE2 sing Y N 27 HIS CE1 HE1 sing N N 28 HIS NE2 HE2 sing N N 29 HIS OXT HXT sing N N 30 ILE N CA sing N N 31 ILE N H sing N N 32 ILE N H2 sing N N 33 ILE CA C sing N N 34 ILE CA CB sing N N 35 ILE CA HA sing N N 36 ILE C O doub N N 37 ILE C OXT sing N N 38 ILE CB CG1 sing N N 39 ILE CB CG2 sing N N 40 ILE CB HB sing N N 41 ILE CG1 CD1 sing N N 42 ILE CG1 HG12 sing N N 43 ILE CG1 HG13 sing N N 44 ILE CG2 HG21 sing N N 45 ILE CG2 HG22 sing N N 46 ILE CG2 HG23 sing N N 47 ILE CD1 HD11 sing N N 48 ILE CD1 HD12 sing N N 49 ILE CD1 HD13 sing N N 50 ILE OXT HXT sing N N 51 MPD C1 C2 sing N N 52 MPD C1 H11 sing N N 53 MPD C1 H12 sing N N 54 MPD C1 H13 sing N N 55 MPD C2 O2 sing N N 56 MPD C2 CM sing N N 57 MPD C2 C3 sing N N 58 MPD O2 HO2 sing N N 59 MPD CM HM1 sing N N 60 MPD CM HM2 sing N N 61 MPD CM HM3 sing N N 62 MPD C3 C4 sing N N 63 MPD C3 H31 sing N N 64 MPD C3 H32 sing N N 65 MPD C4 O4 sing N N 66 MPD C4 C5 sing N N 67 MPD C4 H4 sing N N 68 MPD O4 HO4 sing N N 69 MPD C5 H51 sing N N 70 MPD C5 H52 sing N N 71 MPD C5 H53 sing N N 72 PHE N CA sing N N 73 PHE N H sing N N 74 PHE N H2 sing N N 75 PHE CA C sing N N 76 PHE CA CB sing N N 77 PHE CA HA sing N N 78 PHE C O doub N N 79 PHE C OXT sing N N 80 PHE CB CG sing N N 81 PHE CB HB2 sing N N 82 PHE CB HB3 sing N N 83 PHE CG CD1 doub Y N 84 PHE CG CD2 sing Y N 85 PHE CD1 CE1 sing Y N 86 PHE CD1 HD1 sing N N 87 PHE CD2 CE2 doub Y N 88 PHE CD2 HD2 sing N N 89 PHE CE1 CZ doub Y N 90 PHE CE1 HE1 sing N N 91 PHE CE2 CZ sing Y N 92 PHE CE2 HE2 sing N N 93 PHE CZ HZ sing N N 94 PHE OXT HXT sing N N 95 SER N CA sing N N 96 SER N H sing N N 97 SER N H2 sing N N 98 SER CA C sing N N 99 SER CA CB sing N N 100 SER CA HA sing N N 101 SER C O doub N N 102 SER C OXT sing N N 103 SER CB OG sing N N 104 SER CB HB2 sing N N 105 SER CB HB3 sing N N 106 SER OG HG sing N N 107 SER OXT HXT sing N N 108 # _atom_sites.entry_id 3NVF _atom_sites.fract_transf_matrix[1][1] 0.036303 _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] 0.032240 _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] 0.208160 _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_