data_3N1B # _entry.id 3N1B # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.287 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3N1B RCSB RCSB059254 WWPDB D_1000059254 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 2a2f . unspecified PDB 2fji . unspecified PDB 3fhn . unspecified PDB 2pfv . unspecified PDB 3hr0 . unspecified PDB 3N1E . unspecified # _pdbx_database_status.entry_id 3N1B _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-05-15 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Perez-Victoria, F.J.' 1 'Abascal-Palacios, G.' 2 'Tascon, I.' 3 'Kajava, A.' 4 'Pioro, E.P.' 5 'Bonifacino, J.S.' 6 'Hierro, A.' 7 # _citation.id primary _citation.title 'Structural basis for the wobbler mouse neurodegenerative disorder caused by mutation in the Vps54 subunit of the GARP complex.' _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_volume 107 _citation.page_first 12860 _citation.page_last 12865 _citation.year 2010 _citation.journal_id_ASTM PNASA6 _citation.country US _citation.journal_id_ISSN 0027-8424 _citation.journal_id_CSD 0040 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 20615984 _citation.pdbx_database_id_DOI 10.1073/pnas.1004756107 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Perez-Victoria, F.J.' 1 primary 'Abascal-Palacios, G.' 2 primary 'Tascon, I.' 3 primary 'Kajava, A.' 4 primary 'Magadan, J.G.' 5 primary 'Pioro, E.P.' 6 primary 'Bonifacino, J.S.' 7 primary 'Hierro, A.' 8 # _cell.length_a 125.862 _cell.length_b 30.323 _cell.length_c 88.953 _cell.angle_alpha 90.000 _cell.angle_beta 120.500 _cell.angle_gamma 90.000 _cell.entry_id 3N1B _cell.pdbx_unique_axis ? _cell.Z_PDB 8 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.entry_id 3N1B _symmetry.Int_Tables_number 5 _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 'Vacuolar protein sorting-associated protein 54' 16499.338 2 ? ? 'residues 836-974' ? 2 water nat water 18.015 63 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'Tumor antigen SLP-8p homolog' # _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 ;MDQWSMLRHFDHITKDYHDHIAEISAKLVAI(MSE)DSLFDKLLSKYEVKAPVPSPCFRNICKQ(MSE)TK(MSE)HEAI FDLLPEEQTQ(MSE)LFLRINASYKLHLKKQLSHLNVINDGGPQNGLVTADVAFYTGNLQALKGLKDLDLN(MSE)AEIW E ; _entity_poly.pdbx_seq_one_letter_code_can ;MDQWSMLRHFDHITKDYHDHIAEISAKLVAIMDSLFDKLLSKYEVKAPVPSPCFRNICKQMTKMHEAIFDLLPEEQTQML FLRINASYKLHLKKQLSHLNVINDGGPQNGLVTADVAFYTGNLQALKGLKDLDLNMAEIWE ; _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 ASP n 1 3 GLN n 1 4 TRP n 1 5 SER n 1 6 MET n 1 7 LEU n 1 8 ARG n 1 9 HIS n 1 10 PHE n 1 11 ASP n 1 12 HIS n 1 13 ILE n 1 14 THR n 1 15 LYS n 1 16 ASP n 1 17 TYR n 1 18 HIS n 1 19 ASP n 1 20 HIS n 1 21 ILE n 1 22 ALA n 1 23 GLU n 1 24 ILE n 1 25 SER n 1 26 ALA n 1 27 LYS n 1 28 LEU n 1 29 VAL n 1 30 ALA n 1 31 ILE n 1 32 MSE n 1 33 ASP n 1 34 SER n 1 35 LEU n 1 36 PHE n 1 37 ASP n 1 38 LYS n 1 39 LEU n 1 40 LEU n 1 41 SER n 1 42 LYS n 1 43 TYR n 1 44 GLU n 1 45 VAL n 1 46 LYS n 1 47 ALA n 1 48 PRO n 1 49 VAL n 1 50 PRO n 1 51 SER n 1 52 PRO n 1 53 CYS n 1 54 PHE n 1 55 ARG n 1 56 ASN n 1 57 ILE n 1 58 CYS n 1 59 LYS n 1 60 GLN n 1 61 MSE n 1 62 THR n 1 63 LYS n 1 64 MSE n 1 65 HIS n 1 66 GLU n 1 67 ALA n 1 68 ILE n 1 69 PHE n 1 70 ASP n 1 71 LEU n 1 72 LEU n 1 73 PRO n 1 74 GLU n 1 75 GLU n 1 76 GLN n 1 77 THR n 1 78 GLN n 1 79 MSE n 1 80 LEU n 1 81 PHE n 1 82 LEU n 1 83 ARG n 1 84 ILE n 1 85 ASN n 1 86 ALA n 1 87 SER n 1 88 TYR n 1 89 LYS n 1 90 LEU n 1 91 HIS n 1 92 LEU n 1 93 LYS n 1 94 LYS n 1 95 GLN n 1 96 LEU n 1 97 SER n 1 98 HIS n 1 99 LEU n 1 100 ASN n 1 101 VAL n 1 102 ILE n 1 103 ASN n 1 104 ASP n 1 105 GLY n 1 106 GLY n 1 107 PRO n 1 108 GLN n 1 109 ASN n 1 110 GLY n 1 111 LEU n 1 112 VAL n 1 113 THR n 1 114 ALA n 1 115 ASP n 1 116 VAL n 1 117 ALA n 1 118 PHE n 1 119 TYR n 1 120 THR n 1 121 GLY n 1 122 ASN n 1 123 LEU n 1 124 GLN n 1 125 ALA n 1 126 LEU n 1 127 LYS n 1 128 GLY n 1 129 LEU n 1 130 LYS n 1 131 ASP n 1 132 LEU n 1 133 ASP n 1 134 LEU n 1 135 ASN n 1 136 MSE n 1 137 ALA n 1 138 GLU n 1 139 ILE n 1 140 TRP n 1 141 GLU 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 mouse _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene Vps54 _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 'Mus musculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 10090 _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 'BL21 (DE3)' _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 GST-parallel _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code VPS54_MOUSE _struct_ref.pdbx_db_accession Q5SPW0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;DQWSMLRHFDHITKDYHDHIAEISAKLVAIMDSLFDKLLSKYEVKAPVPSPCFRNICKQMTKMHEAIFDLLPEEQTQMLF LRINASYKLHLKKQLSHLNVINDGGPQNGLVTADVAFYTGNLQALKGLKDLDLNMAEIWE ; _struct_ref.pdbx_align_begin 836 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3N1B A 2 ? 141 ? Q5SPW0 836 ? 975 ? 835 974 2 1 3N1B B 2 ? 141 ? Q5SPW0 836 ? 975 ? 835 974 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 3N1B MET A 1 ? UNP Q5SPW0 ? ? 'EXPRESSION TAG' 834 1 2 3N1B MET B 1 ? UNP Q5SPW0 ? ? 'EXPRESSION TAG' 834 2 # 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 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 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 2 _exptl.entry_id 3N1B _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.23 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 44.94 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.temp 277 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '23% PEG3350, 0.1M BisTris, 0.1M I3C, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K' _exptl_crystal_grow.pdbx_pH_range ? # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 ? ? 1 2 ? ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD 'ADSC QUANTUM 315r' ? ? 2 CCD 'ADSC QUANTUM 315r' ? ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.monochromator _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.pdbx_scattering_type 1 1 'SINGLE WAVELENGTH' ? M x-ray 2 1 MAD ? M x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1.700 1.0 2 0.9791 1.0 3 0.9794 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline 1 SYNCHROTRON 'ESRF BEAMLINE ID23-1' ? 1.700 ESRF ID23-1 2 SYNCHROTRON 'ESRF BEAMLINE ID23-1' ? '0.9791, 0.9794' ESRF ID23-1 # _reflns.entry_id 3N1B _reflns.d_resolution_high 2.398 _reflns.d_resolution_low 50.000 _reflns.number_obs 11565 _reflns.pdbx_Rmerge_I_obs 0.066 _reflns.pdbx_netI_over_sigmaI 18.400 _reflns.pdbx_chi_squared 1.035 _reflns.pdbx_redundancy 3.300 _reflns.percent_possible_obs 98.400 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1,2 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 2.40 2.49 ? ? ? 0.200 ? ? 1.044 2.30 ? 1043 90.30 ? 1 2.49 2.59 ? ? ? 0.168 ? ? 1.040 2.70 ? 1127 96.70 ? 2 2.59 2.70 ? ? ? 0.127 ? ? 1.040 3.10 ? 1139 98.90 ? 3 2.70 2.85 ? ? ? 0.099 ? ? 1.036 3.30 ? 1151 99.80 ? 4 2.85 3.02 ? ? ? 0.083 ? ? 1.039 3.50 ? 1171 99.90 ? 5 3.02 3.26 ? ? ? 0.070 ? ? 1.029 3.60 ? 1161 99.90 ? 6 3.26 3.58 ? ? ? 0.056 ? ? 1.017 3.60 ? 1162 99.90 ? 7 3.58 4.10 ? ? ? 0.056 ? ? 1.041 3.60 ? 1186 100.00 ? 8 4.10 5.17 ? ? ? 0.068 ? ? 1.038 3.50 ? 1195 100.00 ? 9 5.17 50.00 ? ? ? 0.061 ? ? 1.036 3.30 ? 1230 98.60 ? 10 # _refine.entry_id 3N1B _refine.ls_d_res_high 2.398 _refine.ls_d_res_low 30.976 _refine.pdbx_ls_sigma_F 0.00 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 96.050 _refine.ls_number_reflns_obs 11296 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.241 _refine.ls_R_factor_R_work 0.239 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.287 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 4.750 _refine.ls_number_reflns_R_free 536 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 50.553 _refine.solvent_model_param_bsol 43.967 _refine.solvent_model_param_ksol 0.324 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] 1.804 _refine.aniso_B[2][2] -1.056 _refine.aniso_B[3][3] -0.749 _refine.aniso_B[1][2] -0.000 _refine.aniso_B[1][3] -0.488 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.330 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.110 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.900 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct MAD _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.786 _refine.B_iso_max 124.91 _refine.B_iso_min 24.29 _refine.occupancy_max 1.00 _refine.occupancy_min 1.00 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 2103 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 63 _refine_hist.number_atoms_total 2166 _refine_hist.d_res_high 2.398 _refine_hist.d_res_low 30.976 # 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 f_bond_d 2146 0.002 ? ? 'X-RAY DIFFRACTION' ? f_angle_d 2898 0.547 ? ? 'X-RAY DIFFRACTION' ? f_chiral_restr 329 0.038 ? ? 'X-RAY DIFFRACTION' ? f_plane_restr 368 0.002 ? ? 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 795 15.087 ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.d_res_high _refine_ls_shell.d_res_low _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_all _refine_ls_shell.R_factor_R_work _refine_ls_shell.R_factor_R_free _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.number_reflns_all _refine_ls_shell.number_reflns_obs _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.pdbx_refine_id 2.398 2.640 4 88.000 2411 . 0.274 0.334 . 130 . 2541 . . 'X-RAY DIFFRACTION' 2.640 3.021 4 97.000 2700 . 0.254 0.306 . 149 . 2849 . . 'X-RAY DIFFRACTION' 3.021 3.806 4 99.000 2784 . 0.232 0.280 . 118 . 2902 . . 'X-RAY DIFFRACTION' 3.806 30.978 4 99.000 2865 . 0.223 0.267 . 139 . 3004 . . 'X-RAY DIFFRACTION' # _struct.entry_id 3N1B _struct.title 'C-terminal domain of Vps54 subunit of the GARP complex' _struct.pdbx_descriptor 'Vacuolar protein sorting-associated protein 54' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3N1B _struct_keywords.pdbx_keywords 'TRANSPORT PROTEIN' _struct_keywords.text 'spinal muscular atrophy, vesicle trafficking, Golgi apparatus, tethering complex, GARP, TRANSPORT PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_biol.id 1 _struct_biol.details ? # 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 11 ? SER A 41 ? ASP A 844 SER A 874 1 ? 31 HELX_P HELX_P2 2 SER A 51 ? PHE A 69 ? SER A 884 PHE A 902 1 ? 19 HELX_P HELX_P3 3 PRO A 73 ? LEU A 99 ? PRO A 906 LEU A 932 1 ? 27 HELX_P HELX_P4 4 GLY A 106 ? LEU A 126 ? GLY A 939 LEU A 959 1 ? 21 HELX_P HELX_P5 5 ASN A 135 ? TRP A 140 ? ASN A 968 TRP A 973 5 ? 6 HELX_P HELX_P6 6 ILE B 13 ? HIS B 18 ? ILE B 846 HIS B 851 1 ? 6 HELX_P HELX_P7 7 HIS B 20 ? SER B 41 ? HIS B 853 SER B 874 1 ? 22 HELX_P HELX_P8 8 SER B 51 ? ALA B 67 ? SER B 884 ALA B 900 1 ? 17 HELX_P HELX_P9 9 PRO B 73 ? LEU B 99 ? PRO B 906 LEU B 932 1 ? 27 HELX_P HELX_P10 10 GLY B 106 ? GLN B 124 ? GLY B 939 GLN B 957 1 ? 19 HELX_P HELX_P11 11 ASN B 135 ? TRP B 140 ? ASN B 968 TRP B 973 5 ? 6 # _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 covale1 covale ? ? A ILE 31 C ? ? ? 1_555 A MSE 32 N ? ? A ILE 864 A MSE 865 1_555 ? ? ? ? ? ? ? 1.328 ? covale2 covale ? ? A MSE 32 C ? ? ? 1_555 A ASP 33 N ? ? A MSE 865 A ASP 866 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A GLN 60 C ? ? ? 1_555 A MSE 61 N ? ? A GLN 893 A MSE 894 1_555 ? ? ? ? ? ? ? 1.328 ? covale4 covale ? ? A MSE 61 C ? ? ? 1_555 A THR 62 N ? ? A MSE 894 A THR 895 1_555 ? ? ? ? ? ? ? 1.329 ? covale5 covale ? ? A LYS 63 C ? ? ? 1_555 A MSE 64 N ? ? A LYS 896 A MSE 897 1_555 ? ? ? ? ? ? ? 1.330 ? covale6 covale ? ? A MSE 64 C ? ? ? 1_555 A HIS 65 N ? ? A MSE 897 A HIS 898 1_555 ? ? ? ? ? ? ? 1.329 ? covale7 covale ? ? A GLN 78 C ? ? ? 1_555 A MSE 79 N ? ? A GLN 911 A MSE 912 1_555 ? ? ? ? ? ? ? 1.329 ? covale8 covale ? ? A MSE 79 C ? ? ? 1_555 A LEU 80 N ? ? A MSE 912 A LEU 913 1_555 ? ? ? ? ? ? ? 1.329 ? covale9 covale ? ? A ASN 135 C ? ? ? 1_555 A MSE 136 N ? ? A ASN 968 A MSE 969 1_555 ? ? ? ? ? ? ? 1.329 ? covale10 covale ? ? A MSE 136 C ? ? ? 1_555 A ALA 137 N ? ? A MSE 969 A ALA 970 1_555 ? ? ? ? ? ? ? 1.329 ? covale11 covale ? ? B ILE 31 C ? ? ? 1_555 B MSE 32 N ? ? B ILE 864 B MSE 865 1_555 ? ? ? ? ? ? ? 1.329 ? covale12 covale ? ? B MSE 32 C ? ? ? 1_555 B ASP 33 N ? ? B MSE 865 B ASP 866 1_555 ? ? ? ? ? ? ? 1.329 ? covale13 covale ? ? B GLN 60 C ? ? ? 1_555 B MSE 61 N ? ? B GLN 893 B MSE 894 1_555 ? ? ? ? ? ? ? 1.326 ? covale14 covale ? ? B MSE 61 C ? ? ? 1_555 B THR 62 N ? ? B MSE 894 B THR 895 1_555 ? ? ? ? ? ? ? 1.329 ? covale15 covale ? ? B LYS 63 C ? ? ? 1_555 B MSE 64 N ? ? B LYS 896 B MSE 897 1_555 ? ? ? ? ? ? ? 1.328 ? covale16 covale ? ? B MSE 64 C ? ? ? 1_555 B HIS 65 N ? ? B MSE 897 B HIS 898 1_555 ? ? ? ? ? ? ? 1.330 ? covale17 covale ? ? B GLN 78 C ? ? ? 1_555 B MSE 79 N ? ? B GLN 911 B MSE 912 1_555 ? ? ? ? ? ? ? 1.328 ? covale18 covale ? ? B MSE 79 C ? ? ? 1_555 B LEU 80 N ? ? B MSE 912 B LEU 913 1_555 ? ? ? ? ? ? ? 1.329 ? covale19 covale ? ? B ASN 135 C ? ? ? 1_555 B MSE 136 N ? ? B ASN 968 B MSE 969 1_555 ? ? ? ? ? ? ? 1.327 ? covale20 covale ? ? B MSE 136 C ? ? ? 1_555 B ALA 137 N ? ? B MSE 969 B ALA 970 1_555 ? ? ? ? ? ? ? 1.328 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_mon_prot_cis.pdbx_id _struct_mon_prot_cis.label_comp_id _struct_mon_prot_cis.label_seq_id _struct_mon_prot_cis.label_asym_id _struct_mon_prot_cis.label_alt_id _struct_mon_prot_cis.pdbx_PDB_ins_code _struct_mon_prot_cis.auth_comp_id _struct_mon_prot_cis.auth_seq_id _struct_mon_prot_cis.auth_asym_id _struct_mon_prot_cis.pdbx_label_comp_id_2 _struct_mon_prot_cis.pdbx_label_seq_id_2 _struct_mon_prot_cis.pdbx_label_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_ins_code_2 _struct_mon_prot_cis.pdbx_auth_comp_id_2 _struct_mon_prot_cis.pdbx_auth_seq_id_2 _struct_mon_prot_cis.pdbx_auth_asym_id_2 _struct_mon_prot_cis.pdbx_PDB_model_num _struct_mon_prot_cis.pdbx_omega_angle 1 ALA 47 A . ? ALA 880 A PRO 48 A ? PRO 881 A 1 -0.43 2 VAL 49 A . ? VAL 882 A PRO 50 A ? PRO 883 A 1 1.90 3 ALA 47 B . ? ALA 880 B PRO 48 B ? PRO 881 B 1 0.99 4 VAL 49 B . ? VAL 882 B PRO 50 B ? PRO 883 B 1 2.20 # _atom_sites.entry_id 3N1B _atom_sites.fract_transf_matrix[1][1] 0.007945 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.004680 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.032978 _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] 0.013047 _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 MET 1 834 ? ? ? A . n A 1 2 ASP 2 835 ? ? ? A . n A 1 3 GLN 3 836 ? ? ? A . n A 1 4 TRP 4 837 ? ? ? A . n A 1 5 SER 5 838 ? ? ? A . n A 1 6 MET 6 839 ? ? ? A . n A 1 7 LEU 7 840 ? ? ? A . n A 1 8 ARG 8 841 ? ? ? A . n A 1 9 HIS 9 842 ? ? ? A . n A 1 10 PHE 10 843 ? ? ? A . n A 1 11 ASP 11 844 844 ASP ASP A . n A 1 12 HIS 12 845 845 HIS HIS A . n A 1 13 ILE 13 846 846 ILE ILE A . n A 1 14 THR 14 847 847 THR THR A . n A 1 15 LYS 15 848 848 LYS LYS A . n A 1 16 ASP 16 849 849 ASP ASP A . n A 1 17 TYR 17 850 850 TYR TYR A . n A 1 18 HIS 18 851 851 HIS HIS A . n A 1 19 ASP 19 852 852 ASP ASP A . n A 1 20 HIS 20 853 853 HIS HIS A . n A 1 21 ILE 21 854 854 ILE ILE A . n A 1 22 ALA 22 855 855 ALA ALA A . n A 1 23 GLU 23 856 856 GLU GLU A . n A 1 24 ILE 24 857 857 ILE ILE A . n A 1 25 SER 25 858 858 SER SER A . n A 1 26 ALA 26 859 859 ALA ALA A . n A 1 27 LYS 27 860 860 LYS LYS A . n A 1 28 LEU 28 861 861 LEU LEU A . n A 1 29 VAL 29 862 862 VAL VAL A . n A 1 30 ALA 30 863 863 ALA ALA A . n A 1 31 ILE 31 864 864 ILE ILE A . n A 1 32 MSE 32 865 865 MSE MSE A . n A 1 33 ASP 33 866 866 ASP ASP A . n A 1 34 SER 34 867 867 SER SER A . n A 1 35 LEU 35 868 868 LEU LEU A . n A 1 36 PHE 36 869 869 PHE PHE A . n A 1 37 ASP 37 870 870 ASP ASP A . n A 1 38 LYS 38 871 871 LYS LYS A . n A 1 39 LEU 39 872 872 LEU LEU A . n A 1 40 LEU 40 873 873 LEU LEU A . n A 1 41 SER 41 874 874 SER SER A . n A 1 42 LYS 42 875 875 LYS LYS A . n A 1 43 TYR 43 876 876 TYR TYR A . n A 1 44 GLU 44 877 877 GLU GLU A . n A 1 45 VAL 45 878 878 VAL VAL A . n A 1 46 LYS 46 879 879 LYS LYS A . n A 1 47 ALA 47 880 880 ALA ALA A . n A 1 48 PRO 48 881 881 PRO PRO A . n A 1 49 VAL 49 882 882 VAL VAL A . n A 1 50 PRO 50 883 883 PRO PRO A . n A 1 51 SER 51 884 884 SER SER A . n A 1 52 PRO 52 885 885 PRO PRO A . n A 1 53 CYS 53 886 886 CYS CYS A . n A 1 54 PHE 54 887 887 PHE PHE A . n A 1 55 ARG 55 888 888 ARG ARG A . n A 1 56 ASN 56 889 889 ASN ASN A . n A 1 57 ILE 57 890 890 ILE ILE A . n A 1 58 CYS 58 891 891 CYS CYS A . n A 1 59 LYS 59 892 892 LYS LYS A . n A 1 60 GLN 60 893 893 GLN GLN A . n A 1 61 MSE 61 894 894 MSE MSE A . n A 1 62 THR 62 895 895 THR THR A . n A 1 63 LYS 63 896 896 LYS LYS A . n A 1 64 MSE 64 897 897 MSE MSE A . n A 1 65 HIS 65 898 898 HIS HIS A . n A 1 66 GLU 66 899 899 GLU GLU A . n A 1 67 ALA 67 900 900 ALA ALA A . n A 1 68 ILE 68 901 901 ILE ILE A . n A 1 69 PHE 69 902 902 PHE PHE A . n A 1 70 ASP 70 903 903 ASP ASP A . n A 1 71 LEU 71 904 904 LEU LEU A . n A 1 72 LEU 72 905 905 LEU LEU A . n A 1 73 PRO 73 906 906 PRO PRO A . n A 1 74 GLU 74 907 907 GLU GLU A . n A 1 75 GLU 75 908 908 GLU GLU A . n A 1 76 GLN 76 909 909 GLN GLN A . n A 1 77 THR 77 910 910 THR THR A . n A 1 78 GLN 78 911 911 GLN GLN A . n A 1 79 MSE 79 912 912 MSE MSE A . n A 1 80 LEU 80 913 913 LEU LEU A . n A 1 81 PHE 81 914 914 PHE PHE A . n A 1 82 LEU 82 915 915 LEU LEU A . n A 1 83 ARG 83 916 916 ARG ARG A . n A 1 84 ILE 84 917 917 ILE ILE A . n A 1 85 ASN 85 918 918 ASN ASN A . n A 1 86 ALA 86 919 919 ALA ALA A . n A 1 87 SER 87 920 920 SER SER A . n A 1 88 TYR 88 921 921 TYR TYR A . n A 1 89 LYS 89 922 922 LYS LYS A . n A 1 90 LEU 90 923 923 LEU LEU A . n A 1 91 HIS 91 924 924 HIS HIS A . n A 1 92 LEU 92 925 925 LEU LEU A . n A 1 93 LYS 93 926 926 LYS LYS A . n A 1 94 LYS 94 927 927 LYS LYS A . n A 1 95 GLN 95 928 928 GLN GLN A . n A 1 96 LEU 96 929 929 LEU LEU A . n A 1 97 SER 97 930 930 SER SER A . n A 1 98 HIS 98 931 931 HIS HIS A . n A 1 99 LEU 99 932 932 LEU LEU A . n A 1 100 ASN 100 933 933 ASN ASN A . n A 1 101 VAL 101 934 934 VAL VAL A . n A 1 102 ILE 102 935 935 ILE ILE A . n A 1 103 ASN 103 936 936 ASN ASN A . n A 1 104 ASP 104 937 937 ASP ASP A . n A 1 105 GLY 105 938 938 GLY GLY A . n A 1 106 GLY 106 939 939 GLY GLY A . n A 1 107 PRO 107 940 940 PRO PRO A . n A 1 108 GLN 108 941 941 GLN GLN A . n A 1 109 ASN 109 942 942 ASN ASN A . n A 1 110 GLY 110 943 943 GLY GLY A . n A 1 111 LEU 111 944 944 LEU LEU A . n A 1 112 VAL 112 945 945 VAL VAL A . n A 1 113 THR 113 946 946 THR THR A . n A 1 114 ALA 114 947 947 ALA ALA A . n A 1 115 ASP 115 948 948 ASP ASP A . n A 1 116 VAL 116 949 949 VAL VAL A . n A 1 117 ALA 117 950 950 ALA ALA A . n A 1 118 PHE 118 951 951 PHE PHE A . n A 1 119 TYR 119 952 952 TYR TYR A . n A 1 120 THR 120 953 953 THR THR A . n A 1 121 GLY 121 954 954 GLY GLY A . n A 1 122 ASN 122 955 955 ASN ASN A . n A 1 123 LEU 123 956 956 LEU LEU A . n A 1 124 GLN 124 957 957 GLN GLN A . n A 1 125 ALA 125 958 958 ALA ALA A . n A 1 126 LEU 126 959 959 LEU LEU A . n A 1 127 LYS 127 960 960 LYS LYS A . n A 1 128 GLY 128 961 961 GLY GLY A . n A 1 129 LEU 129 962 962 LEU LEU A . n A 1 130 LYS 130 963 963 LYS LYS A . n A 1 131 ASP 131 964 964 ASP ASP A . n A 1 132 LEU 132 965 965 LEU LEU A . n A 1 133 ASP 133 966 966 ASP ASP A . n A 1 134 LEU 134 967 967 LEU LEU A . n A 1 135 ASN 135 968 968 ASN ASN A . n A 1 136 MSE 136 969 969 MSE MSE A . n A 1 137 ALA 137 970 970 ALA ALA A . n A 1 138 GLU 138 971 971 GLU GLU A . n A 1 139 ILE 139 972 972 ILE ILE A . n A 1 140 TRP 140 973 973 TRP TRP A . n A 1 141 GLU 141 974 974 GLU GLU A . n B 1 1 MET 1 834 ? ? ? B . n B 1 2 ASP 2 835 ? ? ? B . n B 1 3 GLN 3 836 ? ? ? B . n B 1 4 TRP 4 837 ? ? ? B . n B 1 5 SER 5 838 ? ? ? B . n B 1 6 MET 6 839 ? ? ? B . n B 1 7 LEU 7 840 ? ? ? B . n B 1 8 ARG 8 841 ? ? ? B . n B 1 9 HIS 9 842 ? ? ? B . n B 1 10 PHE 10 843 843 PHE PHE B . n B 1 11 ASP 11 844 844 ASP ASP B . n B 1 12 HIS 12 845 845 HIS HIS B . n B 1 13 ILE 13 846 846 ILE ILE B . n B 1 14 THR 14 847 847 THR THR B . n B 1 15 LYS 15 848 848 LYS LYS B . n B 1 16 ASP 16 849 849 ASP ASP B . n B 1 17 TYR 17 850 850 TYR TYR B . n B 1 18 HIS 18 851 851 HIS HIS B . n B 1 19 ASP 19 852 852 ASP ASP B . n B 1 20 HIS 20 853 853 HIS HIS B . n B 1 21 ILE 21 854 854 ILE ILE B . n B 1 22 ALA 22 855 855 ALA ALA B . n B 1 23 GLU 23 856 856 GLU GLU B . n B 1 24 ILE 24 857 857 ILE ILE B . n B 1 25 SER 25 858 858 SER SER B . n B 1 26 ALA 26 859 859 ALA ALA B . n B 1 27 LYS 27 860 860 LYS LYS B . n B 1 28 LEU 28 861 861 LEU LEU B . n B 1 29 VAL 29 862 862 VAL VAL B . n B 1 30 ALA 30 863 863 ALA ALA B . n B 1 31 ILE 31 864 864 ILE ILE B . n B 1 32 MSE 32 865 865 MSE MSE B . n B 1 33 ASP 33 866 866 ASP ASP B . n B 1 34 SER 34 867 867 SER SER B . n B 1 35 LEU 35 868 868 LEU LEU B . n B 1 36 PHE 36 869 869 PHE PHE B . n B 1 37 ASP 37 870 870 ASP ASP B . n B 1 38 LYS 38 871 871 LYS LYS B . n B 1 39 LEU 39 872 872 LEU LEU B . n B 1 40 LEU 40 873 873 LEU LEU B . n B 1 41 SER 41 874 874 SER SER B . n B 1 42 LYS 42 875 875 LYS LYS B . n B 1 43 TYR 43 876 876 TYR TYR B . n B 1 44 GLU 44 877 877 GLU GLU B . n B 1 45 VAL 45 878 878 VAL VAL B . n B 1 46 LYS 46 879 879 LYS LYS B . n B 1 47 ALA 47 880 880 ALA ALA B . n B 1 48 PRO 48 881 881 PRO PRO B . n B 1 49 VAL 49 882 882 VAL VAL B . n B 1 50 PRO 50 883 883 PRO PRO B . n B 1 51 SER 51 884 884 SER SER B . n B 1 52 PRO 52 885 885 PRO PRO B . n B 1 53 CYS 53 886 886 CYS CYS B . n B 1 54 PHE 54 887 887 PHE PHE B . n B 1 55 ARG 55 888 888 ARG ARG B . n B 1 56 ASN 56 889 889 ASN ASN B . n B 1 57 ILE 57 890 890 ILE ILE B . n B 1 58 CYS 58 891 891 CYS CYS B . n B 1 59 LYS 59 892 892 LYS LYS B . n B 1 60 GLN 60 893 893 GLN GLN B . n B 1 61 MSE 61 894 894 MSE MSE B . n B 1 62 THR 62 895 895 THR THR B . n B 1 63 LYS 63 896 896 LYS LYS B . n B 1 64 MSE 64 897 897 MSE MSE B . n B 1 65 HIS 65 898 898 HIS HIS B . n B 1 66 GLU 66 899 899 GLU GLU B . n B 1 67 ALA 67 900 900 ALA ALA B . n B 1 68 ILE 68 901 901 ILE ILE B . n B 1 69 PHE 69 902 902 PHE PHE B . n B 1 70 ASP 70 903 903 ASP ASP B . n B 1 71 LEU 71 904 904 LEU LEU B . n B 1 72 LEU 72 905 905 LEU LEU B . n B 1 73 PRO 73 906 906 PRO PRO B . n B 1 74 GLU 74 907 907 GLU GLU B . n B 1 75 GLU 75 908 908 GLU GLU B . n B 1 76 GLN 76 909 909 GLN GLN B . n B 1 77 THR 77 910 910 THR THR B . n B 1 78 GLN 78 911 911 GLN GLN B . n B 1 79 MSE 79 912 912 MSE MSE B . n B 1 80 LEU 80 913 913 LEU LEU B . n B 1 81 PHE 81 914 914 PHE PHE B . n B 1 82 LEU 82 915 915 LEU LEU B . n B 1 83 ARG 83 916 916 ARG ARG B . n B 1 84 ILE 84 917 917 ILE ILE B . n B 1 85 ASN 85 918 918 ASN ASN B . n B 1 86 ALA 86 919 919 ALA ALA B . n B 1 87 SER 87 920 920 SER SER B . n B 1 88 TYR 88 921 921 TYR TYR B . n B 1 89 LYS 89 922 922 LYS LYS B . n B 1 90 LEU 90 923 923 LEU LEU B . n B 1 91 HIS 91 924 924 HIS HIS B . n B 1 92 LEU 92 925 925 LEU LEU B . n B 1 93 LYS 93 926 926 LYS LYS B . n B 1 94 LYS 94 927 927 LYS LYS B . n B 1 95 GLN 95 928 928 GLN GLN B . n B 1 96 LEU 96 929 929 LEU LEU B . n B 1 97 SER 97 930 930 SER SER B . n B 1 98 HIS 98 931 931 HIS HIS B . n B 1 99 LEU 99 932 932 LEU LEU B . n B 1 100 ASN 100 933 933 ASN ASN B . n B 1 101 VAL 101 934 934 VAL VAL B . n B 1 102 ILE 102 935 935 ILE ILE B . n B 1 103 ASN 103 936 936 ASN ASN B . n B 1 104 ASP 104 937 937 ASP ASP B . n B 1 105 GLY 105 938 938 GLY GLY B . n B 1 106 GLY 106 939 939 GLY GLY B . n B 1 107 PRO 107 940 940 PRO PRO B . n B 1 108 GLN 108 941 941 GLN GLN B . n B 1 109 ASN 109 942 942 ASN ASN B . n B 1 110 GLY 110 943 943 GLY GLY B . n B 1 111 LEU 111 944 944 LEU LEU B . n B 1 112 VAL 112 945 945 VAL VAL B . n B 1 113 THR 113 946 946 THR THR B . n B 1 114 ALA 114 947 947 ALA ALA B . n B 1 115 ASP 115 948 948 ASP ASP B . n B 1 116 VAL 116 949 949 VAL VAL B . n B 1 117 ALA 117 950 950 ALA ALA B . n B 1 118 PHE 118 951 951 PHE PHE B . n B 1 119 TYR 119 952 952 TYR TYR B . n B 1 120 THR 120 953 953 THR THR B . n B 1 121 GLY 121 954 954 GLY GLY B . n B 1 122 ASN 122 955 955 ASN ASN B . n B 1 123 LEU 123 956 956 LEU LEU B . n B 1 124 GLN 124 957 957 GLN GLN B . n B 1 125 ALA 125 958 958 ALA ALA B . n B 1 126 LEU 126 959 959 LEU LEU B . n B 1 127 LYS 127 960 960 LYS LYS B . n B 1 128 GLY 128 961 961 GLY GLY B . n B 1 129 LEU 129 962 962 LEU LEU B . n B 1 130 LYS 130 963 963 LYS LYS B . n B 1 131 ASP 131 964 964 ASP ASP B . n B 1 132 LEU 132 965 965 LEU LEU B . n B 1 133 ASP 133 966 966 ASP ASP B . n B 1 134 LEU 134 967 967 LEU LEU B . n B 1 135 ASN 135 968 968 ASN ASN B . n B 1 136 MSE 136 969 969 MSE MSE B . n B 1 137 ALA 137 970 970 ALA ALA B . n B 1 138 GLU 138 971 971 GLU GLU B . n B 1 139 ILE 139 972 972 ILE ILE B . n B 1 140 TRP 140 973 973 TRP TRP B . n B 1 141 GLU 141 974 974 GLU GLU B . n # 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 C 2 HOH 1 2 2 HOH HOH A . C 2 HOH 2 4 4 HOH HOH A . C 2 HOH 3 5 5 HOH HOH A . C 2 HOH 4 6 6 HOH HOH A . C 2 HOH 5 9 9 HOH HOH A . C 2 HOH 6 10 10 HOH HOH A . C 2 HOH 7 14 14 HOH HOH A . C 2 HOH 8 15 15 HOH HOH A . C 2 HOH 9 16 16 HOH HOH A . C 2 HOH 10 19 19 HOH HOH A . C 2 HOH 11 20 20 HOH HOH A . C 2 HOH 12 21 21 HOH HOH A . C 2 HOH 13 24 24 HOH HOH A . C 2 HOH 14 25 25 HOH HOH A . C 2 HOH 15 27 27 HOH HOH A . C 2 HOH 16 28 28 HOH HOH A . C 2 HOH 17 30 30 HOH HOH A . C 2 HOH 18 31 31 HOH HOH A . C 2 HOH 19 32 32 HOH HOH A . C 2 HOH 20 35 35 HOH HOH A . C 2 HOH 21 36 36 HOH HOH A . C 2 HOH 22 38 38 HOH HOH A . C 2 HOH 23 42 42 HOH HOH A . C 2 HOH 24 43 43 HOH HOH A . C 2 HOH 25 47 47 HOH HOH A . C 2 HOH 26 48 48 HOH HOH A . C 2 HOH 27 49 49 HOH HOH A . C 2 HOH 28 51 51 HOH HOH A . C 2 HOH 29 52 52 HOH HOH A . C 2 HOH 30 53 53 HOH HOH A . C 2 HOH 31 54 54 HOH HOH A . C 2 HOH 32 55 55 HOH HOH A . C 2 HOH 33 56 56 HOH HOH A . C 2 HOH 34 57 57 HOH HOH A . C 2 HOH 35 59 59 HOH HOH A . C 2 HOH 36 60 60 HOH HOH A . C 2 HOH 37 62 62 HOH HOH A . C 2 HOH 38 63 63 HOH HOH A . D 2 HOH 1 1 1 HOH HOH B . D 2 HOH 2 3 3 HOH HOH B . D 2 HOH 3 7 7 HOH HOH B . D 2 HOH 4 8 8 HOH HOH B . D 2 HOH 5 11 11 HOH HOH B . D 2 HOH 6 12 12 HOH HOH B . D 2 HOH 7 13 13 HOH HOH B . D 2 HOH 8 17 17 HOH HOH B . D 2 HOH 9 18 18 HOH HOH B . D 2 HOH 10 22 22 HOH HOH B . D 2 HOH 11 23 23 HOH HOH B . D 2 HOH 12 26 26 HOH HOH B . D 2 HOH 13 29 29 HOH HOH B . D 2 HOH 14 33 33 HOH HOH B . D 2 HOH 15 34 34 HOH HOH B . D 2 HOH 16 37 37 HOH HOH B . D 2 HOH 17 39 39 HOH HOH B . D 2 HOH 18 40 40 HOH HOH B . D 2 HOH 19 41 41 HOH HOH B . D 2 HOH 20 44 44 HOH HOH B . D 2 HOH 21 45 45 HOH HOH B . D 2 HOH 22 46 46 HOH HOH B . D 2 HOH 23 50 50 HOH HOH B . D 2 HOH 24 58 58 HOH HOH B . D 2 HOH 25 61 61 HOH HOH B . # 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 32 A MSE 865 ? MET SELENOMETHIONINE 2 A MSE 61 A MSE 894 ? MET SELENOMETHIONINE 3 A MSE 64 A MSE 897 ? MET SELENOMETHIONINE 4 A MSE 79 A MSE 912 ? MET SELENOMETHIONINE 5 A MSE 136 A MSE 969 ? MET SELENOMETHIONINE 6 B MSE 32 B MSE 865 ? MET SELENOMETHIONINE 7 B MSE 61 B MSE 894 ? MET SELENOMETHIONINE 8 B MSE 64 B MSE 897 ? MET SELENOMETHIONINE 9 B MSE 79 B MSE 912 ? MET SELENOMETHIONINE 10 B MSE 136 B MSE 969 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 author_defined_assembly ? monomeric 1 2 author_defined_assembly ? monomeric 1 3 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1 A,C 2 1 B,D 3 1 A,C 3 2 B,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 3 'ABSA (A^2)' 1420 ? 3 MORE -16 ? 3 'SSA (A^2)' 14230 ? # 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' 4_555 -x+1/2,y+1/2,-z -1.0000000000 0.0000000000 0.0000000000 62.9310000000 0.0000000000 1.0000000000 0.0000000000 15.1615000000 0.0000000000 0.0000000000 -1.0000000000 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 2010-07-14 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-08 # _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 ? # 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' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 3 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # _diffrn_reflns.diffrn_id 1 _diffrn_reflns.pdbx_d_res_high 2.600 _diffrn_reflns.pdbx_d_res_low 50.000 _diffrn_reflns.pdbx_number_obs 9115 _diffrn_reflns.pdbx_Rmerge_I_obs 0.070 _diffrn_reflns.pdbx_Rsym_value ? _diffrn_reflns.pdbx_chi_squared 1.02 _diffrn_reflns.av_sigmaI_over_netI 12.34 _diffrn_reflns.pdbx_redundancy 6.30 _diffrn_reflns.pdbx_percent_possible_obs 99.30 _diffrn_reflns.number 57298 _diffrn_reflns.pdbx_observed_criterion ? _diffrn_reflns.limit_h_max ? _diffrn_reflns.limit_h_min ? _diffrn_reflns.limit_k_max ? _diffrn_reflns.limit_k_min ? _diffrn_reflns.limit_l_max ? _diffrn_reflns.limit_l_min ? # loop_ _pdbx_diffrn_reflns_shell.diffrn_id _pdbx_diffrn_reflns_shell.d_res_high _pdbx_diffrn_reflns_shell.d_res_low _pdbx_diffrn_reflns_shell.number_obs _pdbx_diffrn_reflns_shell.rejects _pdbx_diffrn_reflns_shell.Rmerge_I_obs _pdbx_diffrn_reflns_shell.Rsym_value _pdbx_diffrn_reflns_shell.chi_squared _pdbx_diffrn_reflns_shell.redundancy _pdbx_diffrn_reflns_shell.percent_possible_obs 1 5.60 50.00 ? ? 0.037 ? 1.025 6.80 99.20 1 4.45 5.60 ? ? 0.065 ? 1.034 6.80 100.00 1 3.88 4.45 ? ? 0.082 ? 1.023 7.00 100.00 1 3.53 3.88 ? ? 0.087 ? 1.017 7.00 100.00 1 3.28 3.53 ? ? 0.089 ? 1.020 6.90 100.00 1 3.08 3.28 ? ? 0.104 ? 1.043 6.80 100.00 1 2.93 3.08 ? ? 0.115 ? 1.003 6.50 100.00 1 2.80 2.93 ? ? 0.140 ? 1.002 5.90 99.90 1 2.69 2.80 ? ? 0.164 ? 1.006 5.20 99.10 1 2.60 2.69 ? ? 0.188 ? 1.027 3.90 94.60 # _pdbx_phasing_dm.entry_id 3N1B _pdbx_phasing_dm.fom_acentric 0.630 _pdbx_phasing_dm.fom_centric 0.590 _pdbx_phasing_dm.fom 0.620 _pdbx_phasing_dm.reflns_acentric 10298 _pdbx_phasing_dm.reflns_centric 1256 _pdbx_phasing_dm.reflns 11554 # loop_ _pdbx_phasing_dm_shell.d_res_high _pdbx_phasing_dm_shell.d_res_low _pdbx_phasing_dm_shell.delta_phi_final _pdbx_phasing_dm_shell.delta_phi_initial _pdbx_phasing_dm_shell.fom_acentric _pdbx_phasing_dm_shell.fom_centric _pdbx_phasing_dm_shell.fom _pdbx_phasing_dm_shell.reflns_acentric _pdbx_phasing_dm_shell.reflns_centric _pdbx_phasing_dm_shell.reflns 6.900 30.976 ? ? 0.950 0.850 0.930 396 144 540 4.300 6.900 ? ? 0.930 0.810 0.910 1334 250 1584 3.400 4.300 ? ? 0.890 0.750 0.870 1748 233 1981 3.000 3.400 ? ? 0.760 0.590 0.750 1773 194 1967 2.600 3.000 ? ? 0.490 0.380 0.480 3166 304 3470 2.400 2.600 ? ? 0.200 0.130 0.200 1881 131 2012 # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 RESOLVE 2.13 1-Jun-2008 program 'Thomas C. Terwilliger' terwilliger@lanl.gov phasing http://www.solve.lanl.gov/ ? ? 4 PHENIX . ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 5 PDB_EXTRACT 3.100 'Jan. 22, 2010' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 6 MxCuBE . ? ? ? ? 'data collection' ? ? ? 7 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 8 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? 9 CRANK . ? ? ? ? phasing ? ? ? # loop_ _pdbx_validate_close_contact.id _pdbx_validate_close_contact.PDB_model_num _pdbx_validate_close_contact.auth_atom_id_1 _pdbx_validate_close_contact.auth_asym_id_1 _pdbx_validate_close_contact.auth_comp_id_1 _pdbx_validate_close_contact.auth_seq_id_1 _pdbx_validate_close_contact.PDB_ins_code_1 _pdbx_validate_close_contact.label_alt_id_1 _pdbx_validate_close_contact.auth_atom_id_2 _pdbx_validate_close_contact.auth_asym_id_2 _pdbx_validate_close_contact.auth_comp_id_2 _pdbx_validate_close_contact.auth_seq_id_2 _pdbx_validate_close_contact.PDB_ins_code_2 _pdbx_validate_close_contact.label_alt_id_2 _pdbx_validate_close_contact.dist 1 1 O A HOH 2 ? ? O B HOH 37 ? ? 2.00 2 1 O A HOH 6 ? ? O A HOH 28 ? ? 2.01 3 1 NE1 A TRP 973 ? ? O A HOH 59 ? ? 2.19 # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 HIS B 845 ? ? 71.94 -36.10 2 1 TYR B 850 ? ? -78.44 -73.48 # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A MET 834 ? A MET 1 2 1 Y 1 A ASP 835 ? A ASP 2 3 1 Y 1 A GLN 836 ? A GLN 3 4 1 Y 1 A TRP 837 ? A TRP 4 5 1 Y 1 A SER 838 ? A SER 5 6 1 Y 1 A MET 839 ? A MET 6 7 1 Y 1 A LEU 840 ? A LEU 7 8 1 Y 1 A ARG 841 ? A ARG 8 9 1 Y 1 A HIS 842 ? A HIS 9 10 1 Y 1 A PHE 843 ? A PHE 10 11 1 Y 1 B MET 834 ? B MET 1 12 1 Y 1 B ASP 835 ? B ASP 2 13 1 Y 1 B GLN 836 ? B GLN 3 14 1 Y 1 B TRP 837 ? B TRP 4 15 1 Y 1 B SER 838 ? B SER 5 16 1 Y 1 B MET 839 ? B MET 6 17 1 Y 1 B LEU 840 ? B LEU 7 18 1 Y 1 B ARG 841 ? B ARG 8 19 1 Y 1 B HIS 842 ? B HIS 9 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #