data_2QTD # _entry.id 2QTD # _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 2QTD pdb_00002qtd 10.2210/pdb2qtd/pdb RCSB RCSB044030 ? ? WWPDB D_1000044030 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 376479 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 2QTD _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-08-01 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _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 'NMR structure of the protein NP_247299.1: comparison with the crystal structure.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.F' _citation.journal_volume 66 _citation.page_first 1367 _citation.page_last 1380 _citation.year 2010 _citation.journal_id_ASTM ? _citation.country DK _citation.journal_id_ISSN 1744-3091 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20944234 _citation.pdbx_database_id_DOI 10.1107/S1744309110005890 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Jaudzems, K.' 1 ? primary 'Geralt, M.' 2 ? primary 'Serrano, P.' 3 ? primary 'Mohanty, B.' 4 ? primary 'Horst, R.' 5 ? primary 'Pedrini, B.' 6 ? primary 'Elsliger, M.A.' 7 ? primary 'Wilson, I.A.' 8 ? primary 'Wuthrich, K.' 9 ? # _cell.entry_id 2QTD _cell.length_a 35.860 _cell.length_b 54.120 _cell.length_c 56.530 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _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.entry_id 2QTD _symmetry.Int_Tables_number 19 _symmetry.space_group_name_H-M 'P 21 21 21' _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 'Uncharacterized protein MJ0327' 12112.358 1 ? ? ? ? 2 non-polymer syn 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 122.143 1 ? ? ? ? 3 non-polymer syn 'TETRAETHYLENE GLYCOL' 194.226 7 ? ? ? ? 4 water nat water 18.015 65 ? ? ? ? # _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)IN(MSE)KVAIS(MSE)DVDKISNSFEDCKYFLIVRIDDNEVKSTKVIFNDESGKKSIVKENVNAIICKNISEE NYKKFSKKIEIYHAEGDDVDKNISLFIEGELSKISNP ; _entity_poly.pdbx_seq_one_letter_code_can ;GMINMKVAISMDVDKISNSFEDCKYFLIVRIDDNEVKSTKVIFNDESGKKSIVKENVNAIICKNISEENYKKFSKKIEIY HAEGDDVDKNISLFIEGELSKISNP ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 376479 # 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 ILE n 1 4 ASN n 1 5 MSE n 1 6 LYS n 1 7 VAL n 1 8 ALA n 1 9 ILE n 1 10 SER n 1 11 MSE n 1 12 ASP n 1 13 VAL n 1 14 ASP n 1 15 LYS n 1 16 ILE n 1 17 SER n 1 18 ASN n 1 19 SER n 1 20 PHE n 1 21 GLU n 1 22 ASP n 1 23 CYS n 1 24 LYS n 1 25 TYR n 1 26 PHE n 1 27 LEU n 1 28 ILE n 1 29 VAL n 1 30 ARG n 1 31 ILE n 1 32 ASP n 1 33 ASP n 1 34 ASN n 1 35 GLU n 1 36 VAL n 1 37 LYS n 1 38 SER n 1 39 THR n 1 40 LYS n 1 41 VAL n 1 42 ILE n 1 43 PHE n 1 44 ASN n 1 45 ASP n 1 46 GLU n 1 47 SER n 1 48 GLY n 1 49 LYS n 1 50 LYS n 1 51 SER n 1 52 ILE n 1 53 VAL n 1 54 LYS n 1 55 GLU n 1 56 ASN n 1 57 VAL n 1 58 ASN n 1 59 ALA n 1 60 ILE n 1 61 ILE n 1 62 CYS n 1 63 LYS n 1 64 ASN n 1 65 ILE n 1 66 SER n 1 67 GLU n 1 68 GLU n 1 69 ASN n 1 70 TYR n 1 71 LYS n 1 72 LYS n 1 73 PHE n 1 74 SER n 1 75 LYS n 1 76 LYS n 1 77 ILE n 1 78 GLU n 1 79 ILE n 1 80 TYR n 1 81 HIS n 1 82 ALA n 1 83 GLU n 1 84 GLY n 1 85 ASP n 1 86 ASP n 1 87 VAL n 1 88 ASP n 1 89 LYS n 1 90 ASN n 1 91 ILE n 1 92 SER n 1 93 LEU n 1 94 PHE n 1 95 ILE n 1 96 GLU n 1 97 GLY n 1 98 GLU n 1 99 LEU n 1 100 SER n 1 101 LYS n 1 102 ILE n 1 103 SER n 1 104 ASN n 1 105 PRO 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 Methanocaldococcus _entity_src_gen.pdbx_gene_src_gene 'NP_247299.1, MJ0327' _entity_src_gen.gene_src_species 'Methanocaldococcus jannaschii' _entity_src_gen.gene_src_strain 'DSM 2661, JAL-1, JCM 10045, NBRC 100440' _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 'Methanocaldococcus jannaschii DSM 2661' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 243232 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc 43067 _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 HK100 _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 speedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Y327_METJA _struct_ref.pdbx_db_accession Q57773 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MINMKVAISMDVDKISNSFEDCKYFLIVRIDDNEVKSTKVIFNDESGKKSIVKENVNAIICKNISEENYKKFSKKIEIYH AEGDDVDKNISLFIEGELSKISNP ; _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 2QTD _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 105 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q57773 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 104 _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 104 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2QTD _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q57773 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # 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 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 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 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 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 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PG4 non-polymer . 'TETRAETHYLENE GLYCOL' ? 'C8 H18 O5' 194.226 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 TRS non-polymer . 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL 'TRIS BUFFER' 'C4 H12 N O3 1' 122.143 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.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 2QTD # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.26 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 45.68 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details 'NANODROP, 50.0% PEG 200, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _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 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat mirror (vertical focusing)' _diffrn_detector.pdbx_collection_date 2007-07-02 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent (horizontal focusing)' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 0.91837 1.0 2 0.97883 1.0 3 0.97916 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength_list '0.91837, 0.97883, 0.97916' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 2QTD _reflns.d_resolution_high 1.70 _reflns.d_resolution_low 28.262 _reflns.number_obs 12524 _reflns.pdbx_Rmerge_I_obs 0.036 _reflns.pdbx_netI_over_sigmaI 17.570 _reflns.percent_possible_obs 98.500 _reflns.B_iso_Wilson_estimate 28.904 _reflns.observed_criterion_sigma_I -3.00 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # 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_ordinal _reflns_shell.pdbx_diffrn_id 1.70 1.76 5495 ? 2078 0.320 3.1 ? ? ? ? ? 90.20 1 1 1.76 1.83 6840 ? 2326 0.278 3.9 ? ? ? ? ? 99.70 2 1 1.83 1.91 6679 ? 2259 0.209 5.2 ? ? ? ? ? 99.50 3 1 1.91 2.02 7481 ? 2530 0.151 7.4 ? ? ? ? ? 99.70 4 1 2.02 2.14 6531 ? 2221 0.094 11.1 ? ? ? ? ? 100.00 5 1 2.14 2.31 7062 ? 2398 0.065 14.9 ? ? ? ? ? 99.80 6 1 2.31 2.54 6858 ? 2305 0.047 19.3 ? ? ? ? ? 99.70 7 1 2.54 2.90 6758 ? 2292 0.035 25.5 ? ? ? ? ? 99.80 8 1 2.90 3.66 6918 ? 2360 0.023 37.6 ? ? ? ? ? 99.60 9 1 3.66 28.262 6674 ? 2301 0.019 46.6 ? ? ? ? ? 97.10 10 1 # _refine.entry_id 2QTD _refine.ls_d_res_high 1.700 _refine.ls_d_res_low 28.262 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.300 _refine.ls_number_reflns_obs 12479 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. SEVEN PG4 AND ONE TRIS MOLECULE(S) HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. ; _refine.ls_R_factor_obs 0.205 _refine.ls_R_factor_R_work 0.202 _refine.ls_R_factor_R_free 0.255 _refine.ls_percent_reflns_R_free 4.700 _refine.ls_number_reflns_R_free 584 _refine.B_iso_mean 21.164 _refine.aniso_B[1][1] 0.630 _refine.aniso_B[2][2] -2.200 _refine.aniso_B[3][3] 1.580 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.949 _refine.correlation_coeff_Fo_to_Fc_free 0.910 _refine.pdbx_overall_ESU_R 0.123 _refine.pdbx_overall_ESU_R_Free 0.127 _refine.overall_SU_ML 0.086 _refine.overall_SU_B 4.842 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _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 814 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 67 _refine_hist.number_atoms_solvent 65 _refine_hist.number_atoms_total 946 _refine_hist.d_res_high 1.700 _refine_hist.d_res_low 28.262 # 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 923 0.016 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 651 0.005 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1228 1.814 2.004 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1622 1.278 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 117 6.652 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 39 40.205 27.179 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 174 11.860 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 1 0.679 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 138 0.100 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 968 0.006 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 153 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 152 0.178 0.300 ? 'X-RAY DIFFRACTION' ? r_nbd_other 581 0.142 0.300 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 407 0.168 0.500 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 487 0.083 0.500 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 105 0.155 0.500 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 10 0.185 0.300 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 28 0.190 0.300 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 8 0.327 0.500 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 616 2.223 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 217 0.587 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 900 2.785 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 405 5.278 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 320 7.280 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.700 _refine_ls_shell.d_res_low 1.746 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 94.420 _refine_ls_shell.number_reflns_R_work 806 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.232 _refine_ls_shell.R_factor_R_free 0.313 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 40 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.number_reflns_obs 846 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2QTD _struct.title 'Crystal structure of a putative dinitrogenase (mj0327) from methanocaldococcus jannaschii dsm at 1.70 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;Ribonuclease h-like motif fold, iron-molybdenum cofactor, structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, oxidoreductase ; _struct_keywords.pdbx_keywords OXIDOREDUCTASE _struct_keywords.entry_id 2QTD # 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 3 ? E N N 3 ? F N N 3 ? G N N 3 ? H N N 3 ? I N N 3 ? J N N 4 ? # _struct_biol.id 1 _struct_biol.details ;SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. ; # 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 ASP A 45 ? GLU A 55 ? ASP A 44 GLU A 54 1 ? 11 HELX_P HELX_P2 2 SER A 66 ? LYS A 75 ? SER A 65 LYS A 74 1 ? 10 HELX_P HELX_P3 3 ASP A 86 ? GLU A 96 ? ASP A 85 GLU A 95 1 ? 11 # _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 ILE 3 N ? ? A MSE 1 A ILE 2 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale2 covale both ? A ASN 4 C ? ? ? 1_555 A MSE 5 N ? ? A ASN 3 A MSE 4 1_555 ? ? ? ? ? ? ? 1.346 ? ? covale3 covale both ? A MSE 5 C ? ? ? 1_555 A LYS 6 N ? ? A MSE 4 A LYS 5 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale4 covale both ? A SER 10 C ? ? ? 1_555 A MSE 11 N ? ? A SER 9 A MSE 10 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale5 covale both ? A MSE 11 C ? ? ? 1_555 A ASP 12 N ? ? A MSE 10 A ASP 11 1_555 ? ? ? ? ? ? ? 1.335 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # 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 ? parallel A 4 5 ? 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 GLU A 35 ? PHE A 43 ? GLU A 34 PHE A 42 A 2 TYR A 25 ? ASP A 32 ? TYR A 24 ASP A 31 A 3 MSE A 5 ? MSE A 11 ? MSE A 4 MSE A 10 A 4 ALA A 59 ? CYS A 62 ? ALA A 58 CYS A 61 A 5 GLU A 78 ? HIS A 81 ? GLU A 77 HIS A 80 # 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 O GLU A 35 ? O GLU A 34 N ASP A 32 ? N ASP A 31 A 2 3 O ILE A 31 ? O ILE A 30 N MSE A 5 ? N MSE A 4 A 3 4 N ALA A 8 ? N ALA A 7 O ILE A 61 ? O ILE A 60 A 4 5 N ILE A 60 ? N ILE A 59 O TYR A 80 ? O TYR A 79 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A TRS 105 ? 10 'BINDING SITE FOR RESIDUE TRS A 105' AC2 Software A PG4 106 ? 5 'BINDING SITE FOR RESIDUE PG4 A 106' AC3 Software A PG4 107 ? 7 'BINDING SITE FOR RESIDUE PG4 A 107' AC4 Software A PG4 108 ? 8 'BINDING SITE FOR RESIDUE PG4 A 108' AC5 Software A PG4 109 ? 6 'BINDING SITE FOR RESIDUE PG4 A 109' AC6 Software A PG4 110 ? 5 'BINDING SITE FOR RESIDUE PG4 A 110' AC7 Software A PG4 111 ? 2 'BINDING SITE FOR RESIDUE PG4 A 111' AC8 Software A PG4 112 ? 2 'BINDING SITE FOR RESIDUE PG4 A 112' # 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 10 LYS A 6 ? LYS A 5 . ? 3_654 ? 2 AC1 10 ILE A 28 ? ILE A 27 . ? 3_654 ? 3 AC1 10 ARG A 30 ? ARG A 29 . ? 3_654 ? 4 AC1 10 SER A 38 ? SER A 37 . ? 3_654 ? 5 AC1 10 THR A 39 ? THR A 38 . ? 3_654 ? 6 AC1 10 GLU A 55 ? GLU A 54 . ? 3_654 ? 7 AC1 10 SER A 100 ? SER A 99 . ? 1_555 ? 8 AC1 10 PG4 D . ? PG4 A 107 . ? 3_654 ? 9 AC1 10 HOH J . ? HOH A 130 . ? 1_555 ? 10 AC1 10 HOH J . ? HOH A 167 . ? 1_555 ? 11 AC2 5 ASP A 22 ? ASP A 21 . ? 1_555 ? 12 AC2 5 ASN A 56 ? ASN A 55 . ? 2_554 ? 13 AC2 5 VAL A 57 ? VAL A 56 . ? 2_554 ? 14 AC2 5 ASN A 58 ? ASN A 57 . ? 2_554 ? 15 AC2 5 LYS A 76 ? LYS A 75 . ? 2_554 ? 16 AC3 7 LYS A 6 ? LYS A 5 . ? 1_555 ? 17 AC3 7 ARG A 30 ? ARG A 29 . ? 1_555 ? 18 AC3 7 GLU A 55 ? GLU A 54 . ? 1_555 ? 19 AC3 7 GLU A 83 ? GLU A 82 . ? 3_644 ? 20 AC3 7 TRS B . ? TRS A 105 . ? 3_644 ? 21 AC3 7 HOH J . ? HOH A 120 . ? 3_644 ? 22 AC3 7 HOH J . ? HOH A 153 . ? 3_644 ? 23 AC4 8 MSE A 5 ? MSE A 4 . ? 1_555 ? 24 AC4 8 TYR A 80 ? TYR A 79 . ? 1_555 ? 25 AC4 8 LEU A 93 ? LEU A 92 . ? 1_555 ? 26 AC4 8 PHE A 94 ? PHE A 93 . ? 1_555 ? 27 AC4 8 GLY A 97 ? GLY A 96 . ? 1_555 ? 28 AC4 8 GLU A 98 ? GLU A 97 . ? 1_555 ? 29 AC4 8 LEU A 99 ? LEU A 98 . ? 1_555 ? 30 AC4 8 HOH J . ? HOH A 155 . ? 1_555 ? 31 AC5 6 ASP A 88 ? ASP A 87 . ? 1_555 ? 32 AC5 6 ILE A 91 ? ILE A 90 . ? 1_555 ? 33 AC5 6 SER A 92 ? SER A 91 . ? 1_555 ? 34 AC5 6 ILE A 95 ? ILE A 94 . ? 1_555 ? 35 AC5 6 GLU A 96 ? GLU A 95 . ? 1_555 ? 36 AC5 6 HOH J . ? HOH A 175 . ? 1_555 ? 37 AC6 5 LYS A 24 ? LYS A 23 . ? 1_555 ? 38 AC6 5 PHE A 43 ? PHE A 42 . ? 1_555 ? 39 AC6 5 SER A 74 ? SER A 73 . ? 2_554 ? 40 AC6 5 LYS A 75 ? LYS A 74 . ? 2_554 ? 41 AC6 5 LYS A 76 ? LYS A 75 . ? 2_554 ? 42 AC7 2 VAL A 13 ? VAL A 12 . ? 1_555 ? 43 AC7 2 PHE A 43 ? PHE A 42 . ? 1_555 ? 44 AC8 2 TYR A 25 ? TYR A 24 . ? 1_555 ? 45 AC8 2 ASP A 88 ? ASP A 87 . ? 1_555 ? # _atom_sites.entry_id 2QTD _atom_sites.fract_transf_matrix[1][1] 0.027886 _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] 0.018477 _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] 0.017690 _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 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 ILE 3 2 2 ILE ILE A . n A 1 4 ASN 4 3 3 ASN ASN A . n A 1 5 MSE 5 4 4 MSE MSE A . n A 1 6 LYS 6 5 5 LYS LYS A . n A 1 7 VAL 7 6 6 VAL VAL A . n A 1 8 ALA 8 7 7 ALA ALA A . n A 1 9 ILE 9 8 8 ILE ILE A . n A 1 10 SER 10 9 9 SER SER A . n A 1 11 MSE 11 10 10 MSE MSE A . n A 1 12 ASP 12 11 11 ASP ASP A . n A 1 13 VAL 13 12 12 VAL VAL A . n A 1 14 ASP 14 13 13 ASP ASP A . n A 1 15 LYS 15 14 14 LYS LYS A . n A 1 16 ILE 16 15 15 ILE ILE A . n A 1 17 SER 17 16 16 SER SER A . n A 1 18 ASN 18 17 17 ASN ASN A . n A 1 19 SER 19 18 18 SER SER A . n A 1 20 PHE 20 19 19 PHE PHE A . n A 1 21 GLU 21 20 20 GLU GLU A . n A 1 22 ASP 22 21 21 ASP ASP A . n A 1 23 CYS 23 22 22 CYS CYS A . n A 1 24 LYS 24 23 23 LYS LYS A . n A 1 25 TYR 25 24 24 TYR TYR A . n A 1 26 PHE 26 25 25 PHE PHE A . n A 1 27 LEU 27 26 26 LEU LEU A . n A 1 28 ILE 28 27 27 ILE ILE A . n A 1 29 VAL 29 28 28 VAL VAL A . n A 1 30 ARG 30 29 29 ARG ARG A . n A 1 31 ILE 31 30 30 ILE ILE A . n A 1 32 ASP 32 31 31 ASP ASP A . n A 1 33 ASP 33 32 32 ASP ASP A . n A 1 34 ASN 34 33 33 ASN ASN A . n A 1 35 GLU 35 34 34 GLU GLU A . n A 1 36 VAL 36 35 35 VAL VAL A . n A 1 37 LYS 37 36 36 LYS LYS A . n A 1 38 SER 38 37 37 SER SER A . n A 1 39 THR 39 38 38 THR THR A . n A 1 40 LYS 40 39 39 LYS LYS A . n A 1 41 VAL 41 40 40 VAL VAL A . n A 1 42 ILE 42 41 41 ILE ILE A . n A 1 43 PHE 43 42 42 PHE PHE A . n A 1 44 ASN 44 43 43 ASN ASN A . n A 1 45 ASP 45 44 44 ASP ASP A . n A 1 46 GLU 46 45 45 GLU GLU A . n A 1 47 SER 47 46 46 SER SER A . n A 1 48 GLY 48 47 47 GLY GLY A . n A 1 49 LYS 49 48 48 LYS LYS A . n A 1 50 LYS 50 49 49 LYS LYS A . n A 1 51 SER 51 50 50 SER SER A . n A 1 52 ILE 52 51 51 ILE ILE A . n A 1 53 VAL 53 52 52 VAL VAL A . n A 1 54 LYS 54 53 53 LYS LYS A . n A 1 55 GLU 55 54 54 GLU GLU A . n A 1 56 ASN 56 55 55 ASN ASN A . n A 1 57 VAL 57 56 56 VAL VAL A . n A 1 58 ASN 58 57 57 ASN ASN A . n A 1 59 ALA 59 58 58 ALA ALA A . n A 1 60 ILE 60 59 59 ILE ILE A . n A 1 61 ILE 61 60 60 ILE ILE A . n A 1 62 CYS 62 61 61 CYS CYS A . n A 1 63 LYS 63 62 62 LYS LYS A . n A 1 64 ASN 64 63 63 ASN ASN A . n A 1 65 ILE 65 64 64 ILE ILE A . n A 1 66 SER 66 65 65 SER SER A . n A 1 67 GLU 67 66 66 GLU GLU A . n A 1 68 GLU 68 67 67 GLU GLU A . n A 1 69 ASN 69 68 68 ASN ASN A . n A 1 70 TYR 70 69 69 TYR TYR A . n A 1 71 LYS 71 70 70 LYS LYS A . n A 1 72 LYS 72 71 71 LYS LYS A . n A 1 73 PHE 73 72 72 PHE PHE A . n A 1 74 SER 74 73 73 SER SER A . n A 1 75 LYS 75 74 74 LYS LYS A . n A 1 76 LYS 76 75 75 LYS LYS A . n A 1 77 ILE 77 76 76 ILE ILE A . n A 1 78 GLU 78 77 77 GLU GLU A . n A 1 79 ILE 79 78 78 ILE ILE A . n A 1 80 TYR 80 79 79 TYR TYR A . n A 1 81 HIS 81 80 80 HIS HIS A . n A 1 82 ALA 82 81 81 ALA ALA A . n A 1 83 GLU 83 82 82 GLU GLU A . n A 1 84 GLY 84 83 83 GLY GLY A . n A 1 85 ASP 85 84 84 ASP ASP A . n A 1 86 ASP 86 85 85 ASP ASP A . n A 1 87 VAL 87 86 86 VAL VAL A . n A 1 88 ASP 88 87 87 ASP ASP A . n A 1 89 LYS 89 88 88 LYS LYS A . n A 1 90 ASN 90 89 89 ASN ASN A . n A 1 91 ILE 91 90 90 ILE ILE A . n A 1 92 SER 92 91 91 SER SER A . n A 1 93 LEU 93 92 92 LEU LEU A . n A 1 94 PHE 94 93 93 PHE PHE A . n A 1 95 ILE 95 94 94 ILE ILE A . n A 1 96 GLU 96 95 95 GLU GLU A . n A 1 97 GLY 97 96 96 GLY GLY A . n A 1 98 GLU 98 97 97 GLU GLU A . n A 1 99 LEU 99 98 98 LEU LEU A . n A 1 100 SER 100 99 99 SER SER A . n A 1 101 LYS 101 100 100 LYS LYS A . n A 1 102 ILE 102 101 101 ILE ILE A . n A 1 103 SER 103 102 102 SER SER A . n A 1 104 ASN 104 103 103 ASN ASN A . n A 1 105 PRO 105 104 104 PRO PRO 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 TRS 1 105 1 TRS TRS A . C 3 PG4 1 106 2 PG4 PG4 A . D 3 PG4 1 107 3 PG4 PG4 A . E 3 PG4 1 108 4 PG4 PG4 A . F 3 PG4 1 109 5 PG4 PG4 A . G 3 PG4 1 110 6 PG4 PG4 A . H 3 PG4 1 111 7 PG4 PG4 A . I 3 PG4 1 112 8 PG4 PG4 A . J 4 HOH 1 113 9 HOH HOH A . J 4 HOH 2 114 10 HOH HOH A . J 4 HOH 3 115 11 HOH HOH A . J 4 HOH 4 116 12 HOH HOH A . J 4 HOH 5 117 13 HOH HOH A . J 4 HOH 6 118 14 HOH HOH A . J 4 HOH 7 119 15 HOH HOH A . J 4 HOH 8 120 16 HOH HOH A . J 4 HOH 9 121 17 HOH HOH A . J 4 HOH 10 122 18 HOH HOH A . J 4 HOH 11 123 19 HOH HOH A . J 4 HOH 12 124 20 HOH HOH A . J 4 HOH 13 125 21 HOH HOH A . J 4 HOH 14 126 22 HOH HOH A . J 4 HOH 15 127 23 HOH HOH A . J 4 HOH 16 128 24 HOH HOH A . J 4 HOH 17 129 25 HOH HOH A . J 4 HOH 18 130 26 HOH HOH A . J 4 HOH 19 131 27 HOH HOH A . J 4 HOH 20 132 28 HOH HOH A . J 4 HOH 21 133 29 HOH HOH A . J 4 HOH 22 134 30 HOH HOH A . J 4 HOH 23 135 31 HOH HOH A . J 4 HOH 24 136 32 HOH HOH A . J 4 HOH 25 137 33 HOH HOH A . J 4 HOH 26 138 34 HOH HOH A . J 4 HOH 27 139 35 HOH HOH A . J 4 HOH 28 140 36 HOH HOH A . J 4 HOH 29 141 37 HOH HOH A . J 4 HOH 30 142 38 HOH HOH A . J 4 HOH 31 143 39 HOH HOH A . J 4 HOH 32 144 40 HOH HOH A . J 4 HOH 33 145 41 HOH HOH A . J 4 HOH 34 146 42 HOH HOH A . J 4 HOH 35 147 43 HOH HOH A . J 4 HOH 36 148 44 HOH HOH A . J 4 HOH 37 149 45 HOH HOH A . J 4 HOH 38 150 46 HOH HOH A . J 4 HOH 39 151 47 HOH HOH A . J 4 HOH 40 152 48 HOH HOH A . J 4 HOH 41 153 49 HOH HOH A . J 4 HOH 42 154 50 HOH HOH A . J 4 HOH 43 155 51 HOH HOH A . J 4 HOH 44 156 52 HOH HOH A . J 4 HOH 45 157 53 HOH HOH A . J 4 HOH 46 158 54 HOH HOH A . J 4 HOH 47 159 55 HOH HOH A . J 4 HOH 48 160 56 HOH HOH A . J 4 HOH 49 161 57 HOH HOH A . J 4 HOH 50 162 58 HOH HOH A . J 4 HOH 51 163 59 HOH HOH A . J 4 HOH 52 164 60 HOH HOH A . J 4 HOH 53 165 61 HOH HOH A . J 4 HOH 54 166 62 HOH HOH A . J 4 HOH 55 167 63 HOH HOH A . J 4 HOH 56 168 64 HOH HOH A . J 4 HOH 57 169 65 HOH HOH A . J 4 HOH 58 170 66 HOH HOH A . J 4 HOH 59 171 67 HOH HOH A . J 4 HOH 60 172 68 HOH HOH A . J 4 HOH 61 173 69 HOH HOH A . J 4 HOH 62 174 70 HOH HOH A . J 4 HOH 63 175 71 HOH HOH A . J 4 HOH 64 176 72 HOH HOH A . J 4 HOH 65 177 73 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 5 A MSE 4 ? MET SELENOMETHIONINE 3 A MSE 11 A MSE 10 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # 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 2007-08-21 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2019-07-24 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' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Author supporting evidence' 4 3 'Structure model' 'Refinement description' 5 4 'Structure model' 'Data collection' 6 4 'Structure model' 'Derived calculations' 7 4 'Structure model' 'Refinement description' 8 5 'Structure model' 'Database references' 9 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 3 'Structure model' pdbx_struct_assembly_auth_evidence 2 3 'Structure model' software 3 4 'Structure model' software 4 4 'Structure model' struct_conn 5 5 'Structure model' database_2 6 5 'Structure model' struct_ref_seq_dif 7 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 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_software.classification' 4 4 'Structure model' '_software.contact_author' 5 4 'Structure model' '_software.contact_author_email' 6 4 'Structure model' '_software.language' 7 4 'Structure model' '_software.location' 8 4 'Structure model' '_software.name' 9 4 'Structure model' '_software.type' 10 4 'Structure model' '_software.version' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_struct_ref_seq_dif.details' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 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 13.8667 _pdbx_refine_tls.origin_y 1.0359 _pdbx_refine_tls.origin_z -17.3354 _pdbx_refine_tls.T[1][1] -0.0782 _pdbx_refine_tls.T[2][2] -0.0539 _pdbx_refine_tls.T[3][3] -0.0971 _pdbx_refine_tls.T[1][2] -0.0022 _pdbx_refine_tls.T[1][3] -0.0022 _pdbx_refine_tls.T[2][3] 0.0057 _pdbx_refine_tls.L[1][1] 2.2766 _pdbx_refine_tls.L[2][2] 7.5134 _pdbx_refine_tls.L[3][3] 0.9009 _pdbx_refine_tls.L[1][2] 1.0335 _pdbx_refine_tls.L[1][3] 0.6794 _pdbx_refine_tls.L[2][3] 0.6823 _pdbx_refine_tls.S[1][1] 0.0003 _pdbx_refine_tls.S[2][2] 0.0151 _pdbx_refine_tls.S[3][3] -0.0155 _pdbx_refine_tls.S[1][2] 0.0509 _pdbx_refine_tls.S[1][3] 0.0319 _pdbx_refine_tls.S[2][3] 0.0581 _pdbx_refine_tls.S[2][1] -0.0027 _pdbx_refine_tls.S[3][1] -0.0533 _pdbx_refine_tls.S[3][2] -0.0555 _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_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 8 _pdbx_refine_tls_group.end_label_asym_id F _pdbx_refine_tls_group.end_label_seq_id 1 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 7 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 109 _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # _phasing.method MAD # 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 REFMAC 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SOLVE . ? package 'Tom Terwilliger' terwilliger@LANL.gov phasing http://www.solve.lanl.gov/ ? ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html ? ? 5 PDB_EXTRACT 3.00 'March. 27, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 MAR345 CCD ? ? ? ? 'data collection' ? ? ? 7 XDS . ? ? ? ? 'data reduction' ? ? ? 8 # loop_ _pdbx_database_remark.id _pdbx_database_remark.text 300 ; BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. ; 999 ; SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE FOLLOWED BY THE TARGET SEQUENCE. ; # _pdbx_validate_symm_contact.id 1 _pdbx_validate_symm_contact.PDB_model_num 1 _pdbx_validate_symm_contact.auth_atom_id_1 OE1 _pdbx_validate_symm_contact.auth_asym_id_1 A _pdbx_validate_symm_contact.auth_comp_id_1 GLU _pdbx_validate_symm_contact.auth_seq_id_1 54 _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 O3 _pdbx_validate_symm_contact.auth_asym_id_2 A _pdbx_validate_symm_contact.auth_comp_id_2 TRS _pdbx_validate_symm_contact.auth_seq_id_2 105 _pdbx_validate_symm_contact.PDB_ins_code_2 ? _pdbx_validate_symm_contact.label_alt_id_2 ? _pdbx_validate_symm_contact.site_symmetry_2 3_644 _pdbx_validate_symm_contact.dist 2.16 # 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 GLU 45 ? CG ? A GLU 46 CG 2 1 Y 1 A GLU 45 ? CD ? A GLU 46 CD 3 1 Y 1 A GLU 45 ? OE1 ? A GLU 46 OE1 4 1 Y 1 A GLU 45 ? OE2 ? A GLU 46 OE2 5 1 Y 1 A LYS 49 ? NZ ? A LYS 50 NZ 6 1 Y 1 A LYS 53 ? CE ? A LYS 54 CE 7 1 Y 1 A LYS 53 ? NZ ? A LYS 54 NZ 8 1 Y 1 A GLU 67 ? CG ? A GLU 68 CG 9 1 Y 1 A GLU 67 ? CD ? A GLU 68 CD 10 1 Y 1 A GLU 67 ? OE1 ? A GLU 68 OE1 11 1 Y 1 A GLU 67 ? OE2 ? A GLU 68 OE2 12 1 Y 1 A LYS 70 ? CD ? A LYS 71 CD 13 1 Y 1 A LYS 70 ? CE ? A LYS 71 CE 14 1 Y 1 A LYS 70 ? NZ ? A LYS 71 NZ 15 1 Y 1 A LYS 75 ? CE ? A LYS 76 CE 16 1 Y 1 A LYS 75 ? NZ ? A LYS 76 NZ 17 1 Y 1 A LYS 88 ? CD ? A LYS 89 CD 18 1 Y 1 A LYS 88 ? CE ? A LYS 89 CE 19 1 Y 1 A LYS 88 ? NZ ? A LYS 89 NZ 20 1 N 1 A PG4 106 ? O1 ? C PG4 1 O1 21 1 N 1 A PG4 106 ? C1 ? C PG4 1 C1 22 1 N 1 A PG4 107 ? O1 ? D PG4 1 O1 23 1 N 1 A PG4 107 ? C1 ? D PG4 1 C1 24 1 N 1 A PG4 107 ? C2 ? D PG4 1 C2 25 1 N 1 A PG4 107 ? O2 ? D PG4 1 O2 26 1 N 1 A PG4 107 ? C3 ? D PG4 1 C3 27 1 N 1 A PG4 108 ? O1 ? E PG4 1 O1 28 1 N 1 A PG4 108 ? C1 ? E PG4 1 C1 29 1 N 1 A PG4 108 ? C2 ? E PG4 1 C2 30 1 N 1 A PG4 108 ? O2 ? E PG4 1 O2 31 1 N 1 A PG4 108 ? C3 ? E PG4 1 C3 32 1 N 1 A PG4 108 ? O5 ? E PG4 1 O5 33 1 N 1 A PG4 109 ? C5 ? F PG4 1 C5 34 1 N 1 A PG4 109 ? C6 ? F PG4 1 C6 35 1 N 1 A PG4 109 ? O4 ? F PG4 1 O4 36 1 N 1 A PG4 109 ? C7 ? F PG4 1 C7 37 1 N 1 A PG4 109 ? C8 ? F PG4 1 C8 38 1 N 1 A PG4 109 ? O5 ? F PG4 1 O5 39 1 N 1 A PG4 111 ? C4 ? H PG4 1 C4 40 1 N 1 A PG4 111 ? O3 ? H PG4 1 O3 41 1 N 1 A PG4 111 ? C5 ? H PG4 1 C5 42 1 N 1 A PG4 111 ? C6 ? H PG4 1 C6 43 1 N 1 A PG4 111 ? O4 ? H PG4 1 O4 44 1 N 1 A PG4 111 ? C7 ? H PG4 1 C7 45 1 N 1 A PG4 111 ? C8 ? H PG4 1 C8 46 1 N 1 A PG4 111 ? O5 ? H PG4 1 O5 47 1 N 1 A PG4 112 ? C6 ? I PG4 1 C6 48 1 N 1 A PG4 112 ? O4 ? I PG4 1 O4 49 1 N 1 A PG4 112 ? C7 ? I PG4 1 C7 50 1 N 1 A PG4 112 ? C8 ? I PG4 1 C8 51 1 N 1 A PG4 112 ? O5 ? I PG4 1 O5 # _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 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL TRS 3 'TETRAETHYLENE GLYCOL' PG4 4 water HOH # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'gel filtration' _pdbx_struct_assembly_auth_evidence.details ? #