data_3EBT # _entry.id 3EBT # _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 3EBT pdb_00003ebt 10.2210/pdb3ebt/pdb RCSB RCSB049127 ? ? WWPDB D_1000049127 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 390547 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3EBT _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-08-28 _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 ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Joint Center for Structural Genomics' 1 'Joint Center for Structural Genomics (JCSG)' 2 # _citation.id primary _citation.title 'Crystal structure of NTF2-like protein of unknown function (YP_110153.1) from BURKHOLDERIA PSEUDOMALLEI K96243 at 1.30 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 3EBT _cell.length_a 75.730 _cell.length_b 75.730 _cell.length_c 50.070 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _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 3EBT _symmetry.Int_Tables_number 152 _symmetry.space_group_name_H-M 'P 31 2 1' _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 NTF2-like protein' 15122.360 1 ? ? ? ? 2 non-polymer syn 'UNKNOWN LIGAND' ? 2 ? ? ? ? 3 water nat water 18.015 209 ? ? ? ? # _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)SNN(MSE)QTVRESYEAFHRRDLPGVLAALAPDVRWTHPDG(MSE)SPYGLGGTKHGHDEVIAFIRHVPTHIAE (MSE)RLAPDEFIESGERIVVLGTRRVTAVNGRSATLKFVHVWRFENGRAVTFEDHFDTAE(MSE)IRLITA ; _entity_poly.pdbx_seq_one_letter_code_can ;GMSNNMQTVRESYEAFHRRDLPGVLAALAPDVRWTHPDGMSPYGLGGTKHGHDEVIAFIRHVPTHIAEMRLAPDEFIESG ERIVVLGTRRVTAVNGRSATLKFVHVWRFENGRAVTFEDHFDTAEMIRLITA ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 390547 # 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 SER n 1 4 ASN n 1 5 ASN n 1 6 MSE n 1 7 GLN n 1 8 THR n 1 9 VAL n 1 10 ARG n 1 11 GLU n 1 12 SER n 1 13 TYR n 1 14 GLU n 1 15 ALA n 1 16 PHE n 1 17 HIS n 1 18 ARG n 1 19 ARG n 1 20 ASP n 1 21 LEU n 1 22 PRO n 1 23 GLY n 1 24 VAL n 1 25 LEU n 1 26 ALA n 1 27 ALA n 1 28 LEU n 1 29 ALA n 1 30 PRO n 1 31 ASP n 1 32 VAL n 1 33 ARG n 1 34 TRP n 1 35 THR n 1 36 HIS n 1 37 PRO n 1 38 ASP n 1 39 GLY n 1 40 MSE n 1 41 SER n 1 42 PRO n 1 43 TYR n 1 44 GLY n 1 45 LEU n 1 46 GLY n 1 47 GLY n 1 48 THR n 1 49 LYS n 1 50 HIS n 1 51 GLY n 1 52 HIS n 1 53 ASP n 1 54 GLU n 1 55 VAL n 1 56 ILE n 1 57 ALA n 1 58 PHE n 1 59 ILE n 1 60 ARG n 1 61 HIS n 1 62 VAL n 1 63 PRO n 1 64 THR n 1 65 HIS n 1 66 ILE n 1 67 ALA n 1 68 GLU n 1 69 MSE n 1 70 ARG n 1 71 LEU n 1 72 ALA n 1 73 PRO n 1 74 ASP n 1 75 GLU n 1 76 PHE n 1 77 ILE n 1 78 GLU n 1 79 SER n 1 80 GLY n 1 81 GLU n 1 82 ARG n 1 83 ILE n 1 84 VAL n 1 85 VAL n 1 86 LEU n 1 87 GLY n 1 88 THR n 1 89 ARG n 1 90 ARG n 1 91 VAL n 1 92 THR n 1 93 ALA n 1 94 VAL n 1 95 ASN n 1 96 GLY n 1 97 ARG n 1 98 SER n 1 99 ALA n 1 100 THR n 1 101 LEU n 1 102 LYS n 1 103 PHE n 1 104 VAL n 1 105 HIS n 1 106 VAL n 1 107 TRP n 1 108 ARG n 1 109 PHE n 1 110 GLU n 1 111 ASN n 1 112 GLY n 1 113 ARG n 1 114 ALA n 1 115 VAL n 1 116 THR n 1 117 PHE n 1 118 GLU n 1 119 ASP n 1 120 HIS n 1 121 PHE n 1 122 ASP n 1 123 THR n 1 124 ALA n 1 125 GLU n 1 126 MSE n 1 127 ILE n 1 128 ARG n 1 129 LEU n 1 130 ILE n 1 131 THR n 1 132 ALA 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 'Pseudomonas pseudomallei' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'YP_110153.1, BPSS0132' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain ? _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 'Burkholderia pseudomallei K96243' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 272560 _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 ? _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 Q63P16_BURPS _struct_ref.pdbx_db_accession Q63P16 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MSNNMQTVRESYEAFHRRDLPGVLAALAPDVRWTHPDGMSPYGLGGTKHGHDEVIAFIRHVPTHIAEMRLAPDEFIESGE RIVVLGTRRVTAVNGRSATLKFVHVWRFENGRAVTFEDHFDTAEMIRLITA ; _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 3EBT _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 132 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q63P16 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 131 _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 131 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3EBT _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 Q63P16 _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 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 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 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 UNL non-polymer . 'UNKNOWN LIGAND' ? ? ? VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3EBT # _exptl_crystal.id 1 _exptl_crystal.pdbx_mosaicity ? _exptl_crystal.pdbx_mosaicity_esd ? _exptl_crystal.density_Matthews 2.74 _exptl_crystal.density_diffrn ? _exptl_crystal.density_meas ? _exptl_crystal.density_meas_temp ? _exptl_crystal.density_percent_sol 55.12 _exptl_crystal.size_max ? _exptl_crystal.size_mid ? _exptl_crystal.size_min ? _exptl_crystal.size_rad ? _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 ? _exptl_crystal_grow.temp 277 _exptl_crystal_grow.pdbx_details '20.0000% Glycerol, 0.0400M KH2PO4, 16.0000% PEG-8000, No Buffer pH None, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range . _exptl_crystal_grow.temp_details ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.crystal_id 1 _diffrn.ambient_temp_details ? # _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 2008-08-01 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent monochromator (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 0.97848 1.0 3 0.97904 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 0.91837,0.97848,0.97904 _diffrn_source.pdbx_synchrotron_site SSRL _diffrn_source.pdbx_wavelength ? # _reflns.entry_id 3EBT _reflns.d_resolution_high 1.30 _reflns.d_resolution_low 27.431 _reflns.pdbx_number_measured_all 219462 _reflns.number_obs 40949 _reflns.pdbx_Rmerge_I_obs 0.062 _reflns.pdbx_netI_over_sigmaI 9.590 _reflns.percent_possible_obs 99.000 _reflns.pdbx_Rrim_I_all 0.078 _reflns.B_iso_Wilson_estimate 13.652 _reflns.Rmerge_F_obs 0.123 _reflns.observed_criterion_sigma_I -3.00 _reflns.number_all ? _reflns.observed_criterion_sigma_F ? _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_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.pdbx_rejects _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_possible _reflns_shell.number_unique_all _reflns_shell.Rmerge_F_all _reflns_shell.Rmerge_F_obs _reflns_shell.Rmerge_I_all _reflns_shell.meanI_over_sigI_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_Rrim_I_all _reflns_shell.pdbx_Rpim_I_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 1.30 1.35 20629 ? 8321 ? 0.481 2.1 ? ? ? ? 8475 ? ? 0.786 ? ? 98.20 0.607 ? ? 1 1.35 1.40 20256 ? 7268 ? 0.368 2.9 ? ? ? ? 7292 ? ? 0.575 ? ? 99.70 0.461 ? ? 2 1.40 1.46 20912 ? 7465 ? 0.287 3.6 ? ? ? ? 7489 ? ? 0.451 ? ? 99.70 0.358 ? ? 3 1.46 1.54 23058 ? 8200 ? 0.196 5.1 ? ? ? ? 8234 ? ? 0.299 ? ? 99.60 0.246 ? ? 4 1.54 1.64 22952 ? 8105 ? 0.139 7.0 ? ? ? ? 8143 ? ? 0.195 ? ? 99.50 0.173 ? ? 5 1.64 1.76 21287 ? 7488 ? 0.104 9.0 ? ? ? ? 7530 ? ? 0.138 ? ? 99.40 0.130 ? ? 6 1.76 1.94 22999 ? 8053 ? 0.075 12.0 ? ? ? ? 8113 ? ? 0.091 ? ? 99.30 0.094 ? ? 7 1.94 2.22 22462 ? 7830 ? 0.060 15.4 ? ? ? ? 7903 ? ? 0.061 ? ? 99.10 0.074 ? ? 8 2.22 2.80 22642 ? 7843 ? 0.052 18.3 ? ? ? ? 7971 ? ? 0.046 ? ? 98.40 0.065 ? ? 9 2.80 27.431 22265 ? 7739 ? 0.049 20.6 ? ? ? ? 7914 ? ? 0.040 ? ? 97.80 0.061 ? ? 10 # _refine.entry_id 3EBT _refine.ls_d_res_high 1.300 _refine.ls_d_res_low 27.431 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.770 _refine.ls_number_reflns_obs 40924 _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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. TWO DIFFERENT UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED ADJACENT TO EACH OTHER IN THE PUTATIVE ACTIVE SITE. ; _refine.ls_R_factor_obs 0.141 _refine.ls_R_factor_R_work 0.140 _refine.ls_R_factor_R_free 0.162 _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 2061 _refine.ls_number_reflns_R_work 38863 _refine.B_iso_mean 20.271 _refine.aniso_B[1][1] -0.360 _refine.aniso_B[2][2] -0.360 _refine.aniso_B[3][3] 0.550 _refine.aniso_B[1][2] -0.180 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.976 _refine.correlation_coeff_Fo_to_Fc_free 0.972 _refine.pdbx_overall_ESU_R 0.042 _refine.pdbx_overall_ESU_R_Free 0.040 _refine.overall_SU_ML 0.025 _refine.overall_SU_B 1.282 _refine.solvent_model_details 'BABINET MODEL WITH 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.B_iso_max 60.17 _refine.B_iso_min 6.92 _refine.occupancy_max 1.00 _refine.occupancy_min 0.25 _refine.ls_R_factor_all ? _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _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_isotropic_thermal_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_phase_error ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_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 1032 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 12 _refine_hist.number_atoms_solvent 209 _refine_hist.number_atoms_total 1253 _refine_hist.d_res_high 1.300 _refine_hist.d_res_low 27.431 # 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 1165 0.017 0.021 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 798 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1606 1.760 1.922 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1933 1.519 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 160 4.916 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 62 29.561 22.097 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 191 10.642 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 14 12.502 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 176 0.111 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1358 0.009 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 270 0.003 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 196 0.211 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 848 0.180 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 529 0.169 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 637 0.078 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 140 0.124 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 5 0.186 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 29 0.267 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 25 0.101 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 776 2.254 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 282 1.610 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1150 2.950 4.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 495 3.943 6.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 440 4.905 8.000 ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 2245 3.077 3.000 ? 'X-RAY DIFFRACTION' ? r_sphericity_free 226 8.015 3.000 ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded 1919 5.733 3.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.300 _refine_ls_shell.d_res_low 1.334 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 98.910 _refine_ls_shell.number_reflns_R_work 2838 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.190 _refine_ls_shell.R_factor_R_free 0.220 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 154 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 2992 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3EBT _struct.title 'Crystal structure of a ntf2-like protein of unknown function (bpss0132) from burkholderia pseudomallei k96243 at 1.30 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text 'Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, unknown function' _struct_keywords.pdbx_keywords 'UNKNOWN FUNCTION' _struct_keywords.entry_id 3EBT # 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 2 ? D N N 3 ? # _struct_biol.id 1 _struct_biol.details 'AUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER 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 SER A 3 ? ARG A 18 ? SER A 2 ARG A 17 1 ? 16 HELX_P HELX_P2 2 ASP A 20 ? ALA A 26 ? ASP A 19 ALA A 25 1 ? 7 HELX_P HELX_P3 3 PRO A 37 ? GLY A 44 ? PRO A 36 GLY A 43 5 ? 8 HELX_P HELX_P4 4 GLY A 51 ? VAL A 62 ? GLY A 50 VAL A 61 1 ? 12 HELX_P HELX_P5 5 ASP A 122 ? THR A 131 ? ASP A 121 THR A 130 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 GLY 1 C ? ? ? 1_555 A MSE 2 N ? ? A GLY 0 A MSE 1 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale2 covale both ? A MSE 2 C ? ? ? 1_555 A SER 3 N ? ? A MSE 1 A SER 2 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale3 covale both ? A ASN 5 C ? ? ? 1_555 A MSE 6 N ? ? A ASN 4 A MSE 5 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale4 covale both ? A MSE 6 C ? ? ? 1_555 A GLN 7 N ? ? A MSE 5 A GLN 6 1_555 ? ? ? ? ? ? ? 1.351 ? ? covale5 covale both ? A GLY 39 C ? ? ? 1_555 A MSE 40 N ? ? A GLY 38 A MSE 39 1_555 ? ? ? ? ? ? ? 1.343 ? ? covale6 covale both ? A MSE 40 C ? ? ? 1_555 A SER 41 N ? ? A MSE 39 A SER 40 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale7 covale both ? A GLU 68 C ? ? ? 1_555 A MSE 69 N ? ? A GLU 67 A MSE 68 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale8 covale both ? A MSE 69 C ? ? ? 1_555 A ARG 70 N ? ? A MSE 68 A ARG 69 1_555 ? ? ? ? ? ? ? 1.328 ? ? covale9 covale both ? A GLU 125 C ? ? ? 1_555 A MSE 126 N ? ? A GLU 124 A MSE 125 1_555 ? ? ? ? ? ? ? 1.338 ? ? covale10 covale both ? A MSE 126 C ? ? ? 1_555 A ILE 127 N ? ? A MSE 125 A ILE 126 1_555 ? ? ? ? ? ? ? 1.328 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 6 _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 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel A 5 6 ? 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 GLY A 47 ? HIS A 50 ? GLY A 46 HIS A 49 A 2 LEU A 28 ? HIS A 36 ? LEU A 27 HIS A 35 A 3 ARG A 113 ? HIS A 120 ? ARG A 112 HIS A 119 A 4 SER A 98 ? GLU A 110 ? SER A 97 GLU A 109 A 5 ARG A 82 ? ALA A 93 ? ARG A 81 ALA A 92 A 6 ILE A 66 ? SER A 79 ? ILE A 65 SER A 78 # 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 LYS A 49 ? O LYS A 48 N TRP A 34 ? N TRP A 33 A 2 3 N THR A 35 ? N THR A 34 O PHE A 117 ? O PHE A 116 A 3 4 O HIS A 120 ? O HIS A 119 N VAL A 104 ? N VAL A 103 A 4 5 O HIS A 105 ? O HIS A 104 N VAL A 85 ? N VAL A 84 A 5 6 O THR A 88 ? O THR A 87 N ALA A 72 ? N ALA A 71 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id UNL _struct_site.pdbx_auth_seq_id 133 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 8 _struct_site.details 'BINDING SITE FOR RESIDUE UNL A 133' # 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 8 SER A 12 ? SER A 11 . ? 1_555 ? 2 AC1 8 TYR A 13 ? TYR A 12 . ? 1_555 ? 3 AC1 8 HIS A 36 ? HIS A 35 . ? 1_555 ? 4 AC1 8 LEU A 71 ? LEU A 70 . ? 1_555 ? 5 AC1 8 ARG A 89 ? ARG A 88 . ? 1_555 ? 6 AC1 8 HIS A 105 ? HIS A 104 . ? 1_555 ? 7 AC1 8 PHE A 117 ? PHE A 116 . ? 1_555 ? 8 AC1 8 ASP A 119 ? ASP A 118 . ? 1_555 ? # _atom_sites.entry_id 3EBT _atom_sites.fract_transf_matrix[1][1] 0.013205 _atom_sites.fract_transf_matrix[1][2] 0.007624 _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] 0.015248 _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] 0.019972 _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 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 0 GLY GLY A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 SER 3 2 2 SER SER A . n A 1 4 ASN 4 3 3 ASN ASN A . n A 1 5 ASN 5 4 4 ASN ASN A . n A 1 6 MSE 6 5 5 MSE MSE A . n A 1 7 GLN 7 6 6 GLN GLN A . n A 1 8 THR 8 7 7 THR THR A . n A 1 9 VAL 9 8 8 VAL VAL A . n A 1 10 ARG 10 9 9 ARG ARG A . n A 1 11 GLU 11 10 10 GLU GLU A . n A 1 12 SER 12 11 11 SER SER A . n A 1 13 TYR 13 12 12 TYR TYR A . n A 1 14 GLU 14 13 13 GLU GLU A . n A 1 15 ALA 15 14 14 ALA ALA A . n A 1 16 PHE 16 15 15 PHE PHE A . n A 1 17 HIS 17 16 16 HIS HIS A . n A 1 18 ARG 18 17 17 ARG ARG A . n A 1 19 ARG 19 18 18 ARG ARG A . n A 1 20 ASP 20 19 19 ASP ASP A . n A 1 21 LEU 21 20 20 LEU LEU A . n A 1 22 PRO 22 21 21 PRO PRO A . n A 1 23 GLY 23 22 22 GLY GLY A . n A 1 24 VAL 24 23 23 VAL VAL A . n A 1 25 LEU 25 24 24 LEU LEU A . n A 1 26 ALA 26 25 25 ALA ALA A . n A 1 27 ALA 27 26 26 ALA ALA A . n A 1 28 LEU 28 27 27 LEU LEU A . n A 1 29 ALA 29 28 28 ALA ALA A . n A 1 30 PRO 30 29 29 PRO PRO A . n A 1 31 ASP 31 30 30 ASP ASP A . n A 1 32 VAL 32 31 31 VAL VAL A . n A 1 33 ARG 33 32 32 ARG ARG A . n A 1 34 TRP 34 33 33 TRP TRP A . n A 1 35 THR 35 34 34 THR THR A . n A 1 36 HIS 36 35 35 HIS HIS A . n A 1 37 PRO 37 36 36 PRO PRO A . n A 1 38 ASP 38 37 37 ASP ASP A . n A 1 39 GLY 39 38 38 GLY GLY A . n A 1 40 MSE 40 39 39 MSE MSE A . n A 1 41 SER 41 40 40 SER SER A . n A 1 42 PRO 42 41 41 PRO PRO A . n A 1 43 TYR 43 42 42 TYR TYR A . n A 1 44 GLY 44 43 43 GLY GLY A . n A 1 45 LEU 45 44 44 LEU LEU A . n A 1 46 GLY 46 45 45 GLY GLY A . n A 1 47 GLY 47 46 46 GLY GLY A . n A 1 48 THR 48 47 47 THR THR A . n A 1 49 LYS 49 48 48 LYS LYS A . n A 1 50 HIS 50 49 49 HIS HIS A . n A 1 51 GLY 51 50 50 GLY GLY A . n A 1 52 HIS 52 51 51 HIS HIS A . n A 1 53 ASP 53 52 52 ASP ASP A . n A 1 54 GLU 54 53 53 GLU GLU A . n A 1 55 VAL 55 54 54 VAL VAL A . n A 1 56 ILE 56 55 55 ILE ILE A . n A 1 57 ALA 57 56 56 ALA ALA A . n A 1 58 PHE 58 57 57 PHE PHE A . n A 1 59 ILE 59 58 58 ILE ILE A . n A 1 60 ARG 60 59 59 ARG ARG A . n A 1 61 HIS 61 60 60 HIS HIS A . n A 1 62 VAL 62 61 61 VAL VAL A . n A 1 63 PRO 63 62 62 PRO PRO A . n A 1 64 THR 64 63 63 THR THR A . n A 1 65 HIS 65 64 64 HIS HIS A . n A 1 66 ILE 66 65 65 ILE ILE A . n A 1 67 ALA 67 66 66 ALA ALA A . n A 1 68 GLU 68 67 67 GLU GLU A . n A 1 69 MSE 69 68 68 MSE MSE A . n A 1 70 ARG 70 69 69 ARG ARG A . n A 1 71 LEU 71 70 70 LEU LEU A . n A 1 72 ALA 72 71 71 ALA ALA A . n A 1 73 PRO 73 72 72 PRO PRO A . n A 1 74 ASP 74 73 73 ASP ASP A . n A 1 75 GLU 75 74 74 GLU GLU A . n A 1 76 PHE 76 75 75 PHE PHE 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 SER 79 78 78 SER SER A . n A 1 80 GLY 80 79 79 GLY GLY A . n A 1 81 GLU 81 80 80 GLU GLU A . n A 1 82 ARG 82 81 81 ARG ARG A . n A 1 83 ILE 83 82 82 ILE ILE A . n A 1 84 VAL 84 83 83 VAL VAL A . n A 1 85 VAL 85 84 84 VAL VAL A . n A 1 86 LEU 86 85 85 LEU LEU A . n A 1 87 GLY 87 86 86 GLY GLY A . n A 1 88 THR 88 87 87 THR THR A . n A 1 89 ARG 89 88 88 ARG ARG A . n A 1 90 ARG 90 89 89 ARG ARG A . n A 1 91 VAL 91 90 90 VAL VAL A . n A 1 92 THR 92 91 91 THR THR A . n A 1 93 ALA 93 92 92 ALA ALA A . n A 1 94 VAL 94 93 93 VAL VAL A . n A 1 95 ASN 95 94 94 ASN ASN A . n A 1 96 GLY 96 95 95 GLY GLY A . n A 1 97 ARG 97 96 96 ARG ARG A . n A 1 98 SER 98 97 97 SER SER A . n A 1 99 ALA 99 98 98 ALA ALA A . n A 1 100 THR 100 99 99 THR THR A . n A 1 101 LEU 101 100 100 LEU LEU A . n A 1 102 LYS 102 101 101 LYS LYS A . n A 1 103 PHE 103 102 102 PHE PHE A . n A 1 104 VAL 104 103 103 VAL VAL A . n A 1 105 HIS 105 104 104 HIS HIS A . n A 1 106 VAL 106 105 105 VAL VAL A . n A 1 107 TRP 107 106 106 TRP TRP A . n A 1 108 ARG 108 107 107 ARG ARG A . n A 1 109 PHE 109 108 108 PHE PHE A . n A 1 110 GLU 110 109 109 GLU GLU A . n A 1 111 ASN 111 110 110 ASN ASN A . n A 1 112 GLY 112 111 111 GLY GLY A . n A 1 113 ARG 113 112 112 ARG ARG A . n A 1 114 ALA 114 113 113 ALA ALA A . n A 1 115 VAL 115 114 114 VAL VAL A . n A 1 116 THR 116 115 115 THR THR A . n A 1 117 PHE 117 116 116 PHE PHE A . n A 1 118 GLU 118 117 117 GLU GLU A . n A 1 119 ASP 119 118 118 ASP ASP A . n A 1 120 HIS 120 119 119 HIS HIS A . n A 1 121 PHE 121 120 120 PHE PHE A . n A 1 122 ASP 122 121 121 ASP ASP A . n A 1 123 THR 123 122 122 THR THR A . n A 1 124 ALA 124 123 123 ALA ALA A . n A 1 125 GLU 125 124 124 GLU GLU A . n A 1 126 MSE 126 125 125 MSE MSE A . n A 1 127 ILE 127 126 126 ILE ILE A . n A 1 128 ARG 128 127 127 ARG ARG A . n A 1 129 LEU 129 128 128 LEU LEU A . n A 1 130 ILE 130 129 129 ILE ILE A . n A 1 131 THR 131 130 130 THR THR A . n A 1 132 ALA 132 131 131 ALA ALA 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 UNL 1 132 1 UNL UNL A . C 2 UNL 1 133 2 UNL UNL A . D 3 HOH 1 134 3 HOH HOH A . D 3 HOH 2 135 4 HOH HOH A . D 3 HOH 3 136 5 HOH HOH A . D 3 HOH 4 137 6 HOH HOH A . D 3 HOH 5 138 7 HOH HOH A . D 3 HOH 6 139 8 HOH HOH A . D 3 HOH 7 140 9 HOH HOH A . D 3 HOH 8 141 10 HOH HOH A . D 3 HOH 9 142 11 HOH HOH A . D 3 HOH 10 143 12 HOH HOH A . D 3 HOH 11 144 13 HOH HOH A . D 3 HOH 12 145 14 HOH HOH A . D 3 HOH 13 146 15 HOH HOH A . D 3 HOH 14 147 16 HOH HOH A . D 3 HOH 15 148 17 HOH HOH A . D 3 HOH 16 149 18 HOH HOH A . D 3 HOH 17 150 19 HOH HOH A . D 3 HOH 18 151 20 HOH HOH A . D 3 HOH 19 152 21 HOH HOH A . D 3 HOH 20 153 22 HOH HOH A . D 3 HOH 21 154 23 HOH HOH A . D 3 HOH 22 155 24 HOH HOH A . D 3 HOH 23 156 25 HOH HOH A . D 3 HOH 24 157 26 HOH HOH A . D 3 HOH 25 158 27 HOH HOH A . D 3 HOH 26 159 28 HOH HOH A . D 3 HOH 27 160 29 HOH HOH A . D 3 HOH 28 161 30 HOH HOH A . D 3 HOH 29 162 31 HOH HOH A . D 3 HOH 30 163 32 HOH HOH A . D 3 HOH 31 164 33 HOH HOH A . D 3 HOH 32 165 34 HOH HOH A . D 3 HOH 33 166 35 HOH HOH A . D 3 HOH 34 167 36 HOH HOH A . D 3 HOH 35 168 37 HOH HOH A . D 3 HOH 36 169 38 HOH HOH A . D 3 HOH 37 170 39 HOH HOH A . D 3 HOH 38 171 40 HOH HOH A . D 3 HOH 39 172 41 HOH HOH A . D 3 HOH 40 173 42 HOH HOH A . D 3 HOH 41 174 43 HOH HOH A . D 3 HOH 42 175 44 HOH HOH A . D 3 HOH 43 176 45 HOH HOH A . D 3 HOH 44 177 46 HOH HOH A . D 3 HOH 45 178 47 HOH HOH A . D 3 HOH 46 179 48 HOH HOH A . D 3 HOH 47 180 49 HOH HOH A . D 3 HOH 48 181 50 HOH HOH A . D 3 HOH 49 182 51 HOH HOH A . D 3 HOH 50 183 52 HOH HOH A . D 3 HOH 51 184 53 HOH HOH A . D 3 HOH 52 185 54 HOH HOH A . D 3 HOH 53 186 55 HOH HOH A . D 3 HOH 54 187 56 HOH HOH A . D 3 HOH 55 188 57 HOH HOH A . D 3 HOH 56 189 58 HOH HOH A . D 3 HOH 57 190 59 HOH HOH A . D 3 HOH 58 191 60 HOH HOH A . D 3 HOH 59 192 61 HOH HOH A . D 3 HOH 60 193 62 HOH HOH A . D 3 HOH 61 194 63 HOH HOH A . D 3 HOH 62 195 64 HOH HOH A . D 3 HOH 63 196 65 HOH HOH A . D 3 HOH 64 197 66 HOH HOH A . D 3 HOH 65 198 67 HOH HOH A . D 3 HOH 66 199 68 HOH HOH A . D 3 HOH 67 200 69 HOH HOH A . D 3 HOH 68 201 70 HOH HOH A . D 3 HOH 69 202 71 HOH HOH A . D 3 HOH 70 203 72 HOH HOH A . D 3 HOH 71 204 73 HOH HOH A . D 3 HOH 72 205 74 HOH HOH A . D 3 HOH 73 206 75 HOH HOH A . D 3 HOH 74 207 76 HOH HOH A . D 3 HOH 75 208 77 HOH HOH A . D 3 HOH 76 209 78 HOH HOH A . D 3 HOH 77 210 79 HOH HOH A . D 3 HOH 78 211 80 HOH HOH A . D 3 HOH 79 212 81 HOH HOH A . D 3 HOH 80 213 82 HOH HOH A . D 3 HOH 81 214 83 HOH HOH A . D 3 HOH 82 215 84 HOH HOH A . D 3 HOH 83 216 85 HOH HOH A . D 3 HOH 84 217 86 HOH HOH A . D 3 HOH 85 218 87 HOH HOH A . D 3 HOH 86 219 88 HOH HOH A . D 3 HOH 87 220 89 HOH HOH A . D 3 HOH 88 221 90 HOH HOH A . D 3 HOH 89 222 91 HOH HOH A . D 3 HOH 90 223 92 HOH HOH A . D 3 HOH 91 224 93 HOH HOH A . D 3 HOH 92 225 94 HOH HOH A . D 3 HOH 93 226 95 HOH HOH A . D 3 HOH 94 227 96 HOH HOH A . D 3 HOH 95 228 97 HOH HOH A . D 3 HOH 96 229 98 HOH HOH A . D 3 HOH 97 230 99 HOH HOH A . D 3 HOH 98 231 100 HOH HOH A . D 3 HOH 99 232 101 HOH HOH A . D 3 HOH 100 233 102 HOH HOH A . D 3 HOH 101 234 103 HOH HOH A . D 3 HOH 102 235 104 HOH HOH A . D 3 HOH 103 236 105 HOH HOH A . D 3 HOH 104 237 106 HOH HOH A . D 3 HOH 105 238 107 HOH HOH A . D 3 HOH 106 239 108 HOH HOH A . D 3 HOH 107 240 109 HOH HOH A . D 3 HOH 108 241 110 HOH HOH A . D 3 HOH 109 242 111 HOH HOH A . D 3 HOH 110 243 112 HOH HOH A . D 3 HOH 111 244 113 HOH HOH A . D 3 HOH 112 245 114 HOH HOH A . D 3 HOH 113 246 115 HOH HOH A . D 3 HOH 114 247 116 HOH HOH A . D 3 HOH 115 248 117 HOH HOH A . D 3 HOH 116 249 118 HOH HOH A . D 3 HOH 117 250 119 HOH HOH A . D 3 HOH 118 251 120 HOH HOH A . D 3 HOH 119 252 121 HOH HOH A . D 3 HOH 120 253 122 HOH HOH A . D 3 HOH 121 254 123 HOH HOH A . D 3 HOH 122 255 124 HOH HOH A . D 3 HOH 123 256 125 HOH HOH A . D 3 HOH 124 257 126 HOH HOH A . D 3 HOH 125 258 127 HOH HOH A . D 3 HOH 126 259 128 HOH HOH A . D 3 HOH 127 260 129 HOH HOH A . D 3 HOH 128 261 130 HOH HOH A . D 3 HOH 129 262 131 HOH HOH A . D 3 HOH 130 263 132 HOH HOH A . D 3 HOH 131 264 133 HOH HOH A . D 3 HOH 132 265 134 HOH HOH A . D 3 HOH 133 266 135 HOH HOH A . D 3 HOH 134 267 136 HOH HOH A . D 3 HOH 135 268 137 HOH HOH A . D 3 HOH 136 269 138 HOH HOH A . D 3 HOH 137 270 139 HOH HOH A . D 3 HOH 138 271 140 HOH HOH A . D 3 HOH 139 272 141 HOH HOH A . D 3 HOH 140 273 142 HOH HOH A . D 3 HOH 141 274 143 HOH HOH A . D 3 HOH 142 275 144 HOH HOH A . D 3 HOH 143 276 145 HOH HOH A . D 3 HOH 144 277 146 HOH HOH A . D 3 HOH 145 278 147 HOH HOH A . D 3 HOH 146 279 148 HOH HOH A . D 3 HOH 147 280 149 HOH HOH A . D 3 HOH 148 281 150 HOH HOH A . D 3 HOH 149 282 151 HOH HOH A . D 3 HOH 150 283 152 HOH HOH A . D 3 HOH 151 284 153 HOH HOH A . D 3 HOH 152 285 154 HOH HOH A . D 3 HOH 153 286 155 HOH HOH A . D 3 HOH 154 287 156 HOH HOH A . D 3 HOH 155 288 157 HOH HOH A . D 3 HOH 156 289 158 HOH HOH A . D 3 HOH 157 290 159 HOH HOH A . D 3 HOH 158 291 160 HOH HOH A . D 3 HOH 159 292 161 HOH HOH A . D 3 HOH 160 293 162 HOH HOH A . D 3 HOH 161 294 163 HOH HOH A . D 3 HOH 162 295 164 HOH HOH A . D 3 HOH 163 296 165 HOH HOH A . D 3 HOH 164 297 166 HOH HOH A . D 3 HOH 165 298 167 HOH HOH A . D 3 HOH 166 299 168 HOH HOH A . D 3 HOH 167 300 169 HOH HOH A . D 3 HOH 168 301 170 HOH HOH A . D 3 HOH 169 302 171 HOH HOH A . D 3 HOH 170 303 172 HOH HOH A . D 3 HOH 171 304 173 HOH HOH A . D 3 HOH 172 305 174 HOH HOH A . D 3 HOH 173 306 175 HOH HOH A . D 3 HOH 174 307 176 HOH HOH A . D 3 HOH 175 308 177 HOH HOH A . D 3 HOH 176 309 178 HOH HOH A . D 3 HOH 177 310 179 HOH HOH A . D 3 HOH 178 311 180 HOH HOH A . D 3 HOH 179 312 181 HOH HOH A . D 3 HOH 180 313 182 HOH HOH A . D 3 HOH 181 314 183 HOH HOH A . D 3 HOH 182 315 184 HOH HOH A . D 3 HOH 183 316 185 HOH HOH A . D 3 HOH 184 317 186 HOH HOH A . D 3 HOH 185 318 187 HOH HOH A . D 3 HOH 186 319 188 HOH HOH A . D 3 HOH 187 320 189 HOH HOH A . D 3 HOH 188 321 190 HOH HOH A . D 3 HOH 189 322 191 HOH HOH A . D 3 HOH 190 323 192 HOH HOH A . D 3 HOH 191 324 193 HOH HOH A . D 3 HOH 192 325 194 HOH HOH A . D 3 HOH 193 326 195 HOH HOH A . D 3 HOH 194 327 196 HOH HOH A . D 3 HOH 195 328 197 HOH HOH A . D 3 HOH 196 329 198 HOH HOH A . D 3 HOH 197 330 199 HOH HOH A . D 3 HOH 198 331 200 HOH HOH A . D 3 HOH 199 332 201 HOH HOH A . D 3 HOH 200 333 202 HOH HOH A . D 3 HOH 201 334 203 HOH HOH A . D 3 HOH 202 335 204 HOH HOH A . D 3 HOH 203 336 205 HOH HOH A . D 3 HOH 204 337 206 HOH HOH A . D 3 HOH 205 338 207 HOH HOH A . D 3 HOH 206 339 208 HOH HOH A . D 3 HOH 207 340 209 HOH HOH A . D 3 HOH 208 341 210 HOH HOH A . D 3 HOH 209 342 211 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 6 A MSE 5 ? MET SELENOMETHIONINE 3 A MSE 40 A MSE 39 ? MET SELENOMETHIONINE 4 A MSE 69 A MSE 68 ? MET SELENOMETHIONINE 5 A MSE 126 A MSE 125 ? 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 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,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 3320 ? 1 MORE -10 ? 1 'SSA (A^2)' 11940 ? # 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' 5_554 x-y,-y,-z-1/3 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -16.6900000000 # 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 2008-09-30 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 2023-02-01 # _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' 'Refinement description' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Database references' 8 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_unobs_or_zero_occ_atoms 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' # _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 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SOLVE . ? program '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/html_doc/xscale_program.html ? ? 5 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? 7 # _pdbx_entry_details.entry_id 3EBT _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. ; _pdbx_entry_details.has_ligand_of_interest ? # 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 ARG 18 ? CG ? A ARG 19 CG 2 1 Y 1 A ARG 18 ? CD ? A ARG 19 CD 3 1 Y 1 A ARG 18 ? NE ? A ARG 19 NE 4 1 Y 1 A ARG 18 ? CZ ? A ARG 19 CZ 5 1 Y 1 A ARG 18 ? NH1 ? A ARG 19 NH1 6 1 Y 1 A ARG 18 ? NH2 ? A ARG 19 NH2 7 1 Y 1 A GLU 67 ? CD ? A GLU 68 CD 8 1 Y 1 A GLU 67 ? OE1 ? A GLU 68 OE1 9 1 Y 1 A GLU 67 ? OE2 ? A GLU 68 OE2 10 1 Y 1 A ARG 69 ? CD ? A ARG 70 CD 11 1 Y 1 A ARG 69 ? NE ? A ARG 70 NE 12 1 Y 1 A ARG 69 ? CZ ? A ARG 70 CZ 13 1 Y 1 A ARG 69 ? NH1 ? A ARG 70 NH1 14 1 Y 1 A ARG 69 ? NH2 ? A ARG 70 NH2 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'UNKNOWN LIGAND' UNL 3 water HOH #