data_2NVN # _entry.id 2NVN # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _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 2NVN pdb_00002nvn 10.2210/pdb2nvn/pdb RCSB RCSB040357 ? ? WWPDB D_1000040357 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 368396 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 2NVN _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2006-11-13 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of hypothetical protein (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution' _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 ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 2NVN _cell.length_a 82.180 _cell.length_b 82.180 _cell.length_c 80.500 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _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 2NVN _symmetry.Int_Tables_number 96 _symmetry.space_group_name_H-M 'P 43 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.space_group_name_Hall ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.pdbx_ec _entity.pdbx_mutation _entity.pdbx_fragment _entity.details 1 polymer man 'Hypothetical protein' 13531.932 1 ? ? ? ? 2 non-polymer syn GLYCEROL 92.094 1 ? ? ? ? 3 water nat water 18.015 37 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;G(MSE)GRILREGAGWRLGWDETAHRYPGLVGTTDWAVELTAAE(MSE)ADFCRLVQQLAETIAAIAPEL(MSE)PEERL QIEAESALLWLEAEGFADAYELRLILASDRRVEACWPAAAVPALVAATHTLKGF ; _entity_poly.pdbx_seq_one_letter_code_can ;GMGRILREGAGWRLGWDETAHRYPGLVGTTDWAVELTAAEMADFCRLVQQLAETIAAIAPELMPEERLQIEAESALLWLE AEGFADAYELRLILASDRRVEACWPAAAVPALVAATHTLKGF ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 368396 # 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 MSE n 1 3 GLY n 1 4 ARG n 1 5 ILE n 1 6 LEU n 1 7 ARG n 1 8 GLU n 1 9 GLY n 1 10 ALA n 1 11 GLY n 1 12 TRP n 1 13 ARG n 1 14 LEU n 1 15 GLY n 1 16 TRP n 1 17 ASP n 1 18 GLU n 1 19 THR n 1 20 ALA n 1 21 HIS n 1 22 ARG n 1 23 TYR n 1 24 PRO n 1 25 GLY n 1 26 LEU n 1 27 VAL n 1 28 GLY n 1 29 THR n 1 30 THR n 1 31 ASP n 1 32 TRP n 1 33 ALA n 1 34 VAL n 1 35 GLU n 1 36 LEU n 1 37 THR n 1 38 ALA n 1 39 ALA n 1 40 GLU n 1 41 MSE n 1 42 ALA n 1 43 ASP n 1 44 PHE n 1 45 CYS n 1 46 ARG n 1 47 LEU n 1 48 VAL n 1 49 GLN n 1 50 GLN n 1 51 LEU n 1 52 ALA n 1 53 GLU n 1 54 THR n 1 55 ILE n 1 56 ALA n 1 57 ALA n 1 58 ILE n 1 59 ALA n 1 60 PRO n 1 61 GLU n 1 62 LEU n 1 63 MSE n 1 64 PRO n 1 65 GLU n 1 66 GLU n 1 67 ARG n 1 68 LEU n 1 69 GLN n 1 70 ILE n 1 71 GLU n 1 72 ALA n 1 73 GLU n 1 74 SER n 1 75 ALA n 1 76 LEU n 1 77 LEU n 1 78 TRP n 1 79 LEU n 1 80 GLU n 1 81 ALA n 1 82 GLU n 1 83 GLY n 1 84 PHE n 1 85 ALA n 1 86 ASP n 1 87 ALA n 1 88 TYR n 1 89 GLU n 1 90 LEU n 1 91 ARG n 1 92 LEU n 1 93 ILE n 1 94 LEU n 1 95 ALA n 1 96 SER n 1 97 ASP n 1 98 ARG n 1 99 ARG n 1 100 VAL n 1 101 GLU n 1 102 ALA n 1 103 CYS n 1 104 TRP n 1 105 PRO n 1 106 ALA n 1 107 ALA n 1 108 ALA n 1 109 VAL n 1 110 PRO n 1 111 ALA n 1 112 LEU n 1 113 VAL n 1 114 ALA n 1 115 ALA n 1 116 THR n 1 117 HIS n 1 118 THR n 1 119 LEU n 1 120 LYS n 1 121 GLY n 1 122 PHE n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus Synechococcus _entity_src_gen.pdbx_gene_src_gene YP_400729.1 _entity_src_gen.gene_src_species 'Synechococcus elongatus' _entity_src_gen.gene_src_strain 'PCC 7942' _entity_src_gen.gene_src_tissue ? _entity_src_gen.gene_src_tissue_fraction ? _entity_src_gen.gene_src_details ? _entity_src_gen.pdbx_gene_src_fragment ? _entity_src_gen.pdbx_gene_src_scientific_name 'Synechococcus elongatus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 1140 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus Escherichia _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain ? _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q5MZF1_SYNP6 _struct_ref.pdbx_db_accession Q5MZF1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MGRILREGAGWRLGWDETAHRYPGLVGTTDWAVELTAAEMADFCRLVQQLAETIAAIAPELMPEERLQIEAESALLWLEA EGFADAYELRLILASDRRVEACWPAAAVPALVAATHTLKGF ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 2NVN _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 122 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q5MZF1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 121 _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 121 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 2NVN GLY A 1 ? UNP Q5MZF1 ? ? 'expression tag' 0 1 1 2NVN MSE A 2 ? UNP Q5MZF1 MET 1 'modified residue' 1 2 1 2NVN MSE A 41 ? UNP Q5MZF1 MET 40 'modified residue' 40 3 1 2NVN MSE A 63 ? UNP Q5MZF1 MET 62 'modified residue' 62 4 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 GOL non-polymer . GLYCEROL 'GLYCERIN; PROPANE-1,2,3-TRIOL' 'C3 H8 O3' 92.094 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 2NVN _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 5.02 _exptl_crystal.density_percent_sol 75.50 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8.00 _exptl_crystal_grow.pdbx_details '2.5M NaCl, 0.1M Imidazole, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K, pH 8.00' _exptl_crystal_grow.pdbx_pH_range . # _diffrn.id 1 _diffrn.ambient_temp 100.0 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2006-10-09 _diffrn_detector.details 'FIXED-HEIGHT EXIT BEAM, TOROIDAL FOCUSING MIRROR' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'DOUBLE-CRYSTAL SI(111)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.9805 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ALS BEAMLINE 5.0.2' _diffrn_source.pdbx_synchrotron_site ALS _diffrn_source.pdbx_synchrotron_beamline 5.0.2 _diffrn_source.pdbx_wavelength 0.9805 _diffrn_source.pdbx_wavelength_list ? # _reflns.entry_id 2NVN _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 29.050 _reflns.d_resolution_high 2.500 _reflns.number_obs 10011 _reflns.number_all ? _reflns.percent_possible_obs 99.4 _reflns.pdbx_Rmerge_I_obs 0.059 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 13.56 _reflns.B_iso_Wilson_estimate 71.4 _reflns.pdbx_redundancy 6.88 _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 2.50 _reflns_shell.d_res_low 2.59 _reflns_shell.percent_possible_all 97.7 _reflns_shell.Rmerge_I_obs 0.797 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 1.63 _reflns_shell.pdbx_redundancy ? _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all ? _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 2NVN _refine.ls_number_reflns_obs 9972 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 29.05 _refine.ls_d_res_high 2.50 _refine.ls_percent_reflns_obs 99.8 _refine.ls_R_factor_obs 0.209 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.208 _refine.ls_R_factor_R_free 0.227 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.800 _refine.ls_number_reflns_R_free 478 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.953 _refine.correlation_coeff_Fo_to_Fc_free 0.948 _refine.B_iso_mean 26.66 _refine.aniso_B[1][1] -1.14000 _refine.aniso_B[2][2] -1.14000 _refine.aniso_B[3][3] 2.28000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. ; _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.223 _refine.pdbx_overall_ESU_R_Free 0.186 _refine.overall_SU_ML 0.166 _refine.overall_SU_B 15.450 _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_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _refine.pdbx_overall_phase_error ? _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 930 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 6 _refine_hist.number_atoms_solvent 37 _refine_hist.number_atoms_total 973 _refine_hist.d_res_high 2.50 _refine_hist.d_res_low 29.05 # 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 r_bond_refined_d 0.018 0.022 ? 971 'X-RAY DIFFRACTION' ? r_bond_other_d 0.003 0.020 ? 649 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.823 1.962 ? 1326 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.479 3.000 ? 1568 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.126 5.000 ? 124 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 30.169 22.955 ? 44 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 15.189 15.000 ? 151 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 16.381 15.000 ? 10 'X-RAY DIFFRACTION' ? r_chiral_restr 0.108 0.200 ? 149 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.006 0.020 ? 1098 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 207 'X-RAY DIFFRACTION' ? r_nbd_refined 0.181 0.200 ? 152 'X-RAY DIFFRACTION' ? r_nbd_other 0.146 0.200 ? 583 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.162 0.200 ? 427 'X-RAY DIFFRACTION' ? r_nbtor_other 0.079 0.200 ? 532 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.138 0.200 ? 28 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.098 0.200 ? 9 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.216 0.200 ? 39 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.081 0.200 ? 3 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.863 1.500 ? 703 'X-RAY DIFFRACTION' ? r_mcbond_other 0.136 1.500 ? 246 'X-RAY DIFFRACTION' ? r_mcangle_it 1.131 2.000 ? 964 'X-RAY DIFFRACTION' ? r_scbond_it 1.748 3.000 ? 413 'X-RAY DIFFRACTION' ? r_scangle_it 2.653 4.500 ? 360 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 2.50 _refine_ls_shell.d_res_low 2.57 _refine_ls_shell.number_reflns_R_work 709 _refine_ls_shell.R_factor_R_work 0.381 _refine_ls_shell.percent_reflns_obs 100.00 _refine_ls_shell.R_factor_R_free 0.435 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 31 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2NVN _struct.title ;Crystal structure of a protein with a cupin-like fold and unknown function (YP_400729.1) from Synechococcus SP. PCC 7942 (Elongatus) at 2.50 A resolution ; _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;YP_400729.1, hypothetical protein, Structural Genomics, PSI-2, Protein Structure Initiative, Joint Center for Structural Genomics, JCSG, Structural Genomics-Unknown function COMPLEX ; _struct_keywords.pdbx_keywords 'Structural Genomics/Unknown function' _struct_keywords.entry_id 2NVN # 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 ? # _struct_biol.id 1 # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR A 37 ? ALA A 57 ? THR A 36 ALA A 56 1 ? 21 HELX_P HELX_P2 2 ALA A 108 ? HIS A 117 ? ALA A 107 HIS A 116 1 ? 10 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A MSE 2 C ? ? ? 1_555 A GLY 3 N ? ? A MSE 1 A GLY 2 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale2 covale both ? A GLU 40 C ? ? ? 1_555 A MSE 41 N ? ? A GLU 39 A MSE 40 1_555 ? ? ? ? ? ? ? 1.331 ? ? covale3 covale both ? A MSE 41 C ? ? ? 1_555 A ALA 42 N ? ? A MSE 40 A ALA 41 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale4 covale both ? A LEU 62 C ? ? ? 1_555 A MSE 63 N ? ? A LEU 61 A MSE 62 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale5 covale both ? A MSE 63 C ? ? ? 1_555 A PRO 64 N ? ? A MSE 62 A PRO 63 1_555 ? ? ? ? ? ? ? 1.334 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 4 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 ARG A 4 ? GLY A 9 ? ARG A 3 GLY A 8 A 2 TRP A 12 ? ASP A 17 ? TRP A 11 ASP A 16 A 3 GLY A 25 ? GLY A 28 ? GLY A 24 GLY A 27 A 4 ALA A 33 ? LEU A 36 ? ALA A 32 LEU A 35 B 1 LEU A 68 ? GLU A 73 ? LEU A 67 GLU A 72 B 2 LEU A 77 ? PHE A 84 ? LEU A 76 PHE A 83 B 3 ALA A 87 ? LEU A 94 ? ALA A 86 LEU A 93 B 4 GLU A 101 ? TRP A 104 ? GLU A 100 TRP A 103 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 N ARG A 7 ? N ARG A 6 O LEU A 14 ? O LEU A 13 A 2 3 N GLY A 15 ? N GLY A 14 O LEU A 26 ? O LEU A 25 A 3 4 N VAL A 27 ? N VAL A 26 O VAL A 34 ? O VAL A 33 B 1 2 N LEU A 68 ? N LEU A 67 O GLY A 83 ? O GLY A 82 B 2 3 N GLU A 82 ? N GLU A 81 O GLU A 89 ? O GLU A 88 B 3 4 N LEU A 90 ? N LEU A 89 O TRP A 104 ? O TRP A 103 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id GOL _struct_site.pdbx_auth_seq_id 122 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 2 _struct_site.details 'BINDING SITE FOR RESIDUE GOL A 122' # 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 2 ASP A 31 ? ASP A 30 . ? 7_556 ? 2 AC1 2 GLU A 89 ? GLU A 88 . ? 1_555 ? # _atom_sites.entry_id 2NVN _atom_sites.fract_transf_matrix[1][1] 0.01217 _atom_sites.fract_transf_matrix[1][2] 0.00000 _atom_sites.fract_transf_matrix[1][3] 0.00000 _atom_sites.fract_transf_matrix[2][1] 0.00000 _atom_sites.fract_transf_matrix[2][2] 0.01217 _atom_sites.fract_transf_matrix[2][3] 0.00000 _atom_sites.fract_transf_matrix[3][1] 0.00000 _atom_sites.fract_transf_matrix[3][2] 0.00000 _atom_sites.fract_transf_matrix[3][3] 0.01242 _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 N O S SE # 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 0 ? ? ? A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 GLY 3 2 2 GLY GLY A . n A 1 4 ARG 4 3 3 ARG ARG A . n A 1 5 ILE 5 4 4 ILE ILE A . n A 1 6 LEU 6 5 5 LEU LEU A . n A 1 7 ARG 7 6 6 ARG ARG A . n A 1 8 GLU 8 7 7 GLU GLU A . n A 1 9 GLY 9 8 8 GLY GLY A . n A 1 10 ALA 10 9 9 ALA ALA A . n A 1 11 GLY 11 10 10 GLY GLY A . n A 1 12 TRP 12 11 11 TRP TRP A . n A 1 13 ARG 13 12 12 ARG ARG A . n A 1 14 LEU 14 13 13 LEU LEU A . n A 1 15 GLY 15 14 14 GLY GLY A . n A 1 16 TRP 16 15 15 TRP TRP A . n A 1 17 ASP 17 16 16 ASP ASP A . n A 1 18 GLU 18 17 17 GLU GLU A . n A 1 19 THR 19 18 18 THR THR A . n A 1 20 ALA 20 19 19 ALA ALA A . n A 1 21 HIS 21 20 20 HIS HIS A . n A 1 22 ARG 22 21 21 ARG ARG A . n A 1 23 TYR 23 22 22 TYR TYR A . n A 1 24 PRO 24 23 23 PRO PRO A . n A 1 25 GLY 25 24 24 GLY GLY A . n A 1 26 LEU 26 25 25 LEU LEU A . n A 1 27 VAL 27 26 26 VAL VAL A . n A 1 28 GLY 28 27 27 GLY GLY A . n A 1 29 THR 29 28 28 THR THR A . n A 1 30 THR 30 29 29 THR THR A . n A 1 31 ASP 31 30 30 ASP ASP A . n A 1 32 TRP 32 31 31 TRP TRP A . n A 1 33 ALA 33 32 32 ALA ALA A . n A 1 34 VAL 34 33 33 VAL VAL A . n A 1 35 GLU 35 34 34 GLU GLU A . n A 1 36 LEU 36 35 35 LEU LEU A . n A 1 37 THR 37 36 36 THR THR A . n A 1 38 ALA 38 37 37 ALA ALA A . n A 1 39 ALA 39 38 38 ALA ALA A . n A 1 40 GLU 40 39 39 GLU GLU A . n A 1 41 MSE 41 40 40 MSE MSE A . n A 1 42 ALA 42 41 41 ALA ALA A . n A 1 43 ASP 43 42 42 ASP ASP A . n A 1 44 PHE 44 43 43 PHE PHE A . n A 1 45 CYS 45 44 44 CYS CYS A . n A 1 46 ARG 46 45 45 ARG ARG A . n A 1 47 LEU 47 46 46 LEU LEU A . n A 1 48 VAL 48 47 47 VAL VAL A . n A 1 49 GLN 49 48 48 GLN GLN A . n A 1 50 GLN 50 49 49 GLN GLN A . n A 1 51 LEU 51 50 50 LEU LEU A . n A 1 52 ALA 52 51 51 ALA ALA A . n A 1 53 GLU 53 52 52 GLU GLU A . n A 1 54 THR 54 53 53 THR THR A . n A 1 55 ILE 55 54 54 ILE ILE A . n A 1 56 ALA 56 55 55 ALA ALA A . n A 1 57 ALA 57 56 56 ALA ALA A . n A 1 58 ILE 58 57 57 ILE ILE A . n A 1 59 ALA 59 58 58 ALA ALA A . n A 1 60 PRO 60 59 59 PRO PRO A . n A 1 61 GLU 61 60 60 GLU GLU A . n A 1 62 LEU 62 61 61 LEU LEU A . n A 1 63 MSE 63 62 62 MSE MSE A . n A 1 64 PRO 64 63 63 PRO PRO A . n A 1 65 GLU 65 64 64 GLU GLU A . n A 1 66 GLU 66 65 65 GLU GLU A . n A 1 67 ARG 67 66 66 ARG ARG A . n A 1 68 LEU 68 67 67 LEU LEU A . n A 1 69 GLN 69 68 68 GLN GLN A . n A 1 70 ILE 70 69 69 ILE ILE A . n A 1 71 GLU 71 70 70 GLU GLU A . n A 1 72 ALA 72 71 71 ALA ALA A . n A 1 73 GLU 73 72 72 GLU GLU A . n A 1 74 SER 74 73 73 SER SER A . n A 1 75 ALA 75 74 74 ALA ALA A . n A 1 76 LEU 76 75 75 LEU LEU A . n A 1 77 LEU 77 76 76 LEU LEU A . n A 1 78 TRP 78 77 77 TRP TRP A . n A 1 79 LEU 79 78 78 LEU LEU A . n A 1 80 GLU 80 79 79 GLU GLU A . n A 1 81 ALA 81 80 80 ALA ALA A . n A 1 82 GLU 82 81 81 GLU GLU A . n A 1 83 GLY 83 82 82 GLY GLY A . n A 1 84 PHE 84 83 83 PHE PHE A . n A 1 85 ALA 85 84 84 ALA ALA A . n A 1 86 ASP 86 85 85 ASP ASP A . n A 1 87 ALA 87 86 86 ALA ALA A . n A 1 88 TYR 88 87 87 TYR TYR A . n A 1 89 GLU 89 88 88 GLU GLU A . n A 1 90 LEU 90 89 89 LEU LEU A . n A 1 91 ARG 91 90 90 ARG ARG A . n A 1 92 LEU 92 91 91 LEU LEU A . n A 1 93 ILE 93 92 92 ILE ILE A . n A 1 94 LEU 94 93 93 LEU LEU A . n A 1 95 ALA 95 94 94 ALA ALA A . n A 1 96 SER 96 95 95 SER SER A . n A 1 97 ASP 97 96 96 ASP ASP A . n A 1 98 ARG 98 97 97 ARG ARG A . n A 1 99 ARG 99 98 98 ARG ARG A . n A 1 100 VAL 100 99 99 VAL VAL A . n A 1 101 GLU 101 100 100 GLU GLU A . n A 1 102 ALA 102 101 101 ALA ALA A . n A 1 103 CYS 103 102 102 CYS CYS A . n A 1 104 TRP 104 103 103 TRP TRP A . n A 1 105 PRO 105 104 104 PRO PRO A . n A 1 106 ALA 106 105 105 ALA ALA A . n A 1 107 ALA 107 106 106 ALA ALA A . n A 1 108 ALA 108 107 107 ALA ALA A . n A 1 109 VAL 109 108 108 VAL VAL A . n A 1 110 PRO 110 109 109 PRO PRO A . n A 1 111 ALA 111 110 110 ALA ALA A . n A 1 112 LEU 112 111 111 LEU LEU A . n A 1 113 VAL 113 112 112 VAL VAL A . n A 1 114 ALA 114 113 113 ALA ALA A . n A 1 115 ALA 115 114 114 ALA ALA A . n A 1 116 THR 116 115 115 THR THR A . n A 1 117 HIS 117 116 116 HIS HIS A . n A 1 118 THR 118 117 117 THR THR A . n A 1 119 LEU 119 118 118 LEU LEU A . n A 1 120 LYS 120 119 119 LYS LYS A . n A 1 121 GLY 121 120 120 GLY GLY A . n A 1 122 PHE 122 121 121 PHE PHE A . n # _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # 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 B 2 GOL 1 122 1 GOL GOL A . C 3 HOH 1 123 2 HOH HOH A . C 3 HOH 2 124 3 HOH HOH A . C 3 HOH 3 125 4 HOH HOH A . C 3 HOH 4 126 5 HOH HOH A . C 3 HOH 5 127 6 HOH HOH A . C 3 HOH 6 128 7 HOH HOH A . C 3 HOH 7 129 8 HOH HOH A . C 3 HOH 8 130 9 HOH HOH A . C 3 HOH 9 131 10 HOH HOH A . C 3 HOH 10 132 11 HOH HOH A . C 3 HOH 11 133 12 HOH HOH A . C 3 HOH 12 134 13 HOH HOH A . C 3 HOH 13 135 14 HOH HOH A . C 3 HOH 14 136 15 HOH HOH A . C 3 HOH 15 137 16 HOH HOH A . C 3 HOH 16 138 17 HOH HOH A . C 3 HOH 17 139 18 HOH HOH A . C 3 HOH 18 140 19 HOH HOH A . C 3 HOH 19 141 20 HOH HOH A . C 3 HOH 20 142 21 HOH HOH A . C 3 HOH 21 143 22 HOH HOH A . C 3 HOH 22 144 23 HOH HOH A . C 3 HOH 23 145 24 HOH HOH A . C 3 HOH 24 146 25 HOH HOH A . C 3 HOH 25 147 26 HOH HOH A . C 3 HOH 26 148 27 HOH HOH A . C 3 HOH 27 149 28 HOH HOH A . C 3 HOH 28 150 29 HOH HOH A . C 3 HOH 29 151 30 HOH HOH A . C 3 HOH 30 152 31 HOH HOH A . C 3 HOH 31 153 32 HOH HOH A . C 3 HOH 32 154 33 HOH HOH A . C 3 HOH 33 155 34 HOH HOH A . C 3 HOH 34 156 35 HOH HOH A . C 3 HOH 35 157 36 HOH HOH A . C 3 HOH 36 158 37 HOH HOH A . C 3 HOH 37 159 39 HOH HOH A . # 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 MSE 2 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 41 A MSE 40 ? MET SELENOMETHIONINE 3 A MSE 63 A MSE 62 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _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 # 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' 7_556 y,x,-z+1 0.0000000000 1.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 80.5000000000 # 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 2006-12-12 2 'Structure model' 1 1 2008-05-01 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-18 5 'Structure model' 1 4 2023-01-25 # _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' Advisory 3 3 'Structure model' 'Source and taxonomy' 4 3 'Structure model' 'Version format compliance' 5 4 'Structure model' 'Refinement description' 6 5 'Structure model' 'Database references' 7 5 '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 4 'Structure model' software 2 5 'Structure model' database_2 3 5 'Structure model' struct_conn 4 5 'Structure model' struct_ref_seq_dif 5 5 '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 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' 3 5 'Structure model' '_database_2.pdbx_DOI' 4 5 'Structure model' '_database_2.pdbx_database_accession' 5 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 6 5 'Structure model' '_struct_ref_seq_dif.details' 7 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 8 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 9 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 13.6180 _pdbx_refine_tls.origin_y 23.4880 _pdbx_refine_tls.origin_z 29.8140 _pdbx_refine_tls.T[1][1] 0.3425 _pdbx_refine_tls.T[2][2] 0.3513 _pdbx_refine_tls.T[3][3] 0.0305 _pdbx_refine_tls.T[1][2] -0.0992 _pdbx_refine_tls.T[1][3] -0.0374 _pdbx_refine_tls.T[2][3] 0.0163 _pdbx_refine_tls.L[1][1] 3.6133 _pdbx_refine_tls.L[2][2] 5.6788 _pdbx_refine_tls.L[3][3] 5.5905 _pdbx_refine_tls.L[1][2] -1.1120 _pdbx_refine_tls.L[1][3] 2.1403 _pdbx_refine_tls.L[2][3] -3.1778 _pdbx_refine_tls.S[1][1] 0.2312 _pdbx_refine_tls.S[1][2] 0.1975 _pdbx_refine_tls.S[1][3] -0.2486 _pdbx_refine_tls.S[2][1] -0.6194 _pdbx_refine_tls.S[2][2] 0.1222 _pdbx_refine_tls.S[2][3] 0.3860 _pdbx_refine_tls.S[3][1] 0.2356 _pdbx_refine_tls.S[3][2] -0.3572 _pdbx_refine_tls.S[3][3] -0.3534 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.beg_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 2 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 121 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 122 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # _phasing.method SAD # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 1 SHELX . ? package 'George Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 2 REFMAC 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 3 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html ? ? 4 PDB_EXTRACT 2.000 'April. 3, 2006' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 5 XDS . ? ? ? ? 'data reduction' ? ? ? 6 SHELXD . ? ? ? ? phasing ? ? ? 7 autoSHARP . ? ? ? ? phasing ? ? ? 8 # _pdbx_database_remark.id 300 _pdbx_database_remark.text ; BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ASSIGNMENT OF BIOMOLECULE AS A DIMER IS BASED UPON EBI/PISA ANALYSIS. ; # loop_ _pdbx_validate_rmsd_angle.id _pdbx_validate_rmsd_angle.PDB_model_num _pdbx_validate_rmsd_angle.auth_atom_id_1 _pdbx_validate_rmsd_angle.auth_asym_id_1 _pdbx_validate_rmsd_angle.auth_comp_id_1 _pdbx_validate_rmsd_angle.auth_seq_id_1 _pdbx_validate_rmsd_angle.PDB_ins_code_1 _pdbx_validate_rmsd_angle.label_alt_id_1 _pdbx_validate_rmsd_angle.auth_atom_id_2 _pdbx_validate_rmsd_angle.auth_asym_id_2 _pdbx_validate_rmsd_angle.auth_comp_id_2 _pdbx_validate_rmsd_angle.auth_seq_id_2 _pdbx_validate_rmsd_angle.PDB_ins_code_2 _pdbx_validate_rmsd_angle.label_alt_id_2 _pdbx_validate_rmsd_angle.auth_atom_id_3 _pdbx_validate_rmsd_angle.auth_asym_id_3 _pdbx_validate_rmsd_angle.auth_comp_id_3 _pdbx_validate_rmsd_angle.auth_seq_id_3 _pdbx_validate_rmsd_angle.PDB_ins_code_3 _pdbx_validate_rmsd_angle.label_alt_id_3 _pdbx_validate_rmsd_angle.angle_value _pdbx_validate_rmsd_angle.angle_target_value _pdbx_validate_rmsd_angle.angle_deviation _pdbx_validate_rmsd_angle.angle_standard_deviation _pdbx_validate_rmsd_angle.linker_flag 1 1 NE A ARG 21 ? A CZ A ARG 21 ? A NH1 A ARG 21 ? A 123.31 120.30 3.01 0.50 N 2 1 NE A ARG 97 ? ? CZ A ARG 97 ? ? NH1 A ARG 97 ? ? 124.80 120.30 4.50 0.50 N 3 1 NE A ARG 97 ? ? CZ A ARG 97 ? ? NH2 A ARG 97 ? ? 116.15 120.30 -4.15 0.50 N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 ALA A 86 ? ? -168.13 94.68 2 1 ASP A 96 ? ? 49.08 -131.69 3 1 LEU A 118 ? ? -101.67 75.22 # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A HIS 20 ? CG ? A HIS 21 CG 2 1 Y 1 A HIS 20 ? ND1 ? A HIS 21 ND1 3 1 Y 1 A HIS 20 ? CD2 ? A HIS 21 CD2 4 1 Y 1 A HIS 20 ? CE1 ? A HIS 21 CE1 5 1 Y 1 A HIS 20 ? NE2 ? A HIS 21 NE2 6 1 Y 1 A LYS 119 ? CD ? A LYS 120 CD 7 1 Y 1 A LYS 119 ? CE ? A LYS 120 CE 8 1 Y 1 A LYS 119 ? NZ ? A LYS 120 NZ # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id GLY _pdbx_unobs_or_zero_occ_residues.auth_seq_id 0 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id GLY _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 GLYCEROL GOL 3 water HOH #