data_4DB5 # _entry.id 4DB5 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.281 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 4DB5 RCSB RCSB070109 WWPDB D_1000070109 # _pdbx_database_related.db_name TargetTrack _pdbx_database_related.db_id NYSGRC-011123 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 4DB5 _pdbx_database_status.status_code REL _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2012-01-13 _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Kumar, P.R.' 1 'Bhosle, R.' 2 'Gizzi, A.' 3 'Scott Glenn, A.' 4 'Chowhury, S.' 5 'Hillerich, B.' 6 'Seidel, R.' 7 'Nathenson, S.G.' 8 'Almo, S.C.' 9 'New York Structural Genomics Research Consortium (NYSGRC)' 10 'Atoms-to-Animals: The Immune Function Network (IFN)' 11 # _citation.id primary _citation.title 'Crystal structure of GITRL from Oryctolagus cuniculus' _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 ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Kumar, P.R.' 1 primary 'Bhosle, R.' 2 primary 'Gizzi, A.' 3 primary 'Scott Glenn, A.' 4 primary 'Chowhury, S.' 5 primary 'Hillerich, B.' 6 primary 'Seidel, R.' 7 primary 'Nathenson, S.G.' 8 primary 'Almo, S.C.' 9 # _cell.entry_id 4DB5 _cell.length_a 127.047 _cell.length_b 127.047 _cell.length_c 127.047 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 48 _cell.pdbx_unique_axis ? _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 4DB5 _symmetry.space_group_name_H-M 'F 2 3' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 196 _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 'Tumor necrosis factor ligand superfamily member 18' 14055.084 1 ? ? ? ? 2 non-polymer syn '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' 282.334 1 ? ? ? ? 3 water nat water 18.015 122 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code ;TAKEACVAKFGPLPSKWQMEPPKPSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTLTNNSK IQNLGGIYEFDAGDIIELRFNSDDQVLKNNTYWGIVLLVTPQFSS ; _entity_poly.pdbx_seq_one_letter_code_can ;TAKEACVAKFGPLPSKWQMEPPKPSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTLTNNSK IQNLGGIYEFDAGDIIELRFNSDDQVLKNNTYWGIVLLVTPQFSS ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier NYSGRC-011123 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 THR n 1 2 ALA n 1 3 LYS n 1 4 GLU n 1 5 ALA n 1 6 CYS n 1 7 VAL n 1 8 ALA n 1 9 LYS n 1 10 PHE n 1 11 GLY n 1 12 PRO n 1 13 LEU n 1 14 PRO n 1 15 SER n 1 16 LYS n 1 17 TRP n 1 18 GLN n 1 19 MET n 1 20 GLU n 1 21 PRO n 1 22 PRO n 1 23 LYS n 1 24 PRO n 1 25 SER n 1 26 CYS n 1 27 VAL n 1 28 ASN n 1 29 LYS n 1 30 ILE n 1 31 SER n 1 32 ASP n 1 33 TRP n 1 34 LYS n 1 35 LEU n 1 36 LYS n 1 37 ILE n 1 38 LEU n 1 39 GLN n 1 40 ASN n 1 41 GLY n 1 42 LEU n 1 43 TYR n 1 44 ILE n 1 45 ILE n 1 46 TYR n 1 47 GLY n 1 48 GLN n 1 49 VAL n 1 50 ALA n 1 51 PRO n 1 52 ASP n 1 53 PRO n 1 54 THR n 1 55 TYR n 1 56 LYS n 1 57 GLY n 1 58 PHE n 1 59 ALA n 1 60 PRO n 1 61 PHE n 1 62 GLU n 1 63 VAL n 1 64 GLN n 1 65 LEU n 1 66 CYS n 1 67 LYS n 1 68 ASN n 1 69 LYS n 1 70 GLU n 1 71 ALA n 1 72 ILE n 1 73 GLN n 1 74 THR n 1 75 LEU n 1 76 THR n 1 77 ASN n 1 78 ASN n 1 79 SER n 1 80 LYS n 1 81 ILE n 1 82 GLN n 1 83 ASN n 1 84 LEU n 1 85 GLY n 1 86 GLY n 1 87 ILE n 1 88 TYR n 1 89 GLU n 1 90 PHE n 1 91 ASP n 1 92 ALA n 1 93 GLY n 1 94 ASP n 1 95 ILE n 1 96 ILE n 1 97 GLU n 1 98 LEU n 1 99 ARG n 1 100 PHE n 1 101 ASN n 1 102 SER n 1 103 ASP n 1 104 ASP n 1 105 GLN n 1 106 VAL n 1 107 LEU n 1 108 LYS n 1 109 ASN n 1 110 ASN n 1 111 THR n 1 112 TYR n 1 113 TRP n 1 114 GLY n 1 115 ILE n 1 116 VAL n 1 117 LEU n 1 118 LEU n 1 119 VAL n 1 120 THR n 1 121 PRO n 1 122 GLN n 1 123 PHE n 1 124 SER n 1 125 SER 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 'European rabbit,Japanese white rabbit,domestic rabbit,rabbits' _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'GITRL, TNFSF18' _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 'Oryctolagus cuniculus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9986 _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 469008 _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 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 pET28b _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code G1TIM1_RABIT _struct_ref.pdbx_db_accession G1TIM1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;TAKEACVAKFGPLPSKWQMEPPKPSCVNKISDWKLKILQNGLYIIYGQVAPDPTYKGFAPFEVQLCKNKEAIQTLTNNSK IQNLGGIYEFDAGDIIELRFNSDDQVLKNNTYWGIVLLVTPQFSS ; _struct_ref.pdbx_align_begin 54 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 4DB5 _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 125 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession G1TIM1 _struct_ref_seq.db_align_beg 54 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 178 _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 125 # 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 B3P non-polymer . '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' ? 'C11 H26 N2 O6' 282.334 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 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 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 1 _exptl.entry_id 4DB5 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 3.04 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 59.53 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP' _exptl_crystal_grow.pH 7.0 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details ;Protein (20 mM Hepes, pH 7.5, 150 mM NaCl, 10% glycerol; Reservoir (0.1M Bis-Tris Propane pH 7.0, 2.4M DL-Malic acid); Cryoprotection (Reservoir + 30% glycerol), Sitting Drop, Vapor Diffusion, temperature 298K, VAPOR DIFFUSION, SITTING DROP ; _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC QUANTUM 315' _diffrn_detector.pdbx_collection_date 2011-09-27 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator GRAPHITE _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0750 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'NSLS BEAMLINE X29A' _diffrn_source.pdbx_wavelength_list 1.0750 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site NSLS _diffrn_source.pdbx_synchrotron_beamline X29A # _reflns.entry_id 4DB5 _reflns.d_resolution_high 1.520 _reflns.d_resolution_low 50.000 _reflns.number_obs 26128 _reflns.pdbx_Rmerge_I_obs 0.051 _reflns.pdbx_netI_over_sigmaI 12.500 _reflns.pdbx_chi_squared 1.044 _reflns.pdbx_redundancy 33.100 _reflns.percent_possible_obs 100.000 _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_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.520 1.550 ? ? ? 0.688 ? ? 0.986 32.800 ? 1301 100.000 1 1 1.550 1.570 ? ? ? 0.612 ? ? 0.958 33.000 ? 1278 100.000 2 1 1.570 1.600 ? ? ? 0.490 ? ? 0.971 32.800 ? 1329 100.000 3 1 1.600 1.640 ? ? ? 0.436 ? ? 0.975 33.000 ? 1286 100.000 4 1 1.640 1.670 ? ? ? 0.364 ? ? 0.998 33.100 ? 1291 100.000 5 1 1.670 1.710 ? ? ? 0.336 ? ? 1.016 33.200 ? 1296 100.000 6 1 1.710 1.750 ? ? ? 0.264 ? ? 1.038 33.300 ? 1296 100.000 7 1 1.750 1.800 ? ? ? 0.207 ? ? 1.072 33.200 ? 1295 100.000 8 1 1.800 1.860 ? ? ? 0.168 ? ? 1.067 33.400 ? 1293 100.000 9 1 1.860 1.920 ? ? ? 0.142 ? ? 1.125 33.300 ? 1310 100.000 10 1 1.920 1.980 ? ? ? 0.104 ? ? 1.101 33.300 ? 1297 100.000 11 1 1.980 2.060 ? ? ? 0.082 ? ? 1.076 33.400 ? 1289 100.000 12 1 2.060 2.160 ? ? ? 0.068 ? ? 1.064 33.400 ? 1333 100.000 13 1 2.160 2.270 ? ? ? 0.059 ? ? 1.048 33.300 ? 1276 100.000 14 1 2.270 2.410 ? ? ? 0.051 ? ? 1.000 33.500 ? 1323 100.000 15 1 2.410 2.600 ? ? ? 0.052 ? ? 1.159 33.400 ? 1296 100.000 16 1 2.600 2.860 ? ? ? 0.051 ? ? 1.437 33.000 ? 1328 100.000 17 1 2.860 3.270 ? ? ? 0.042 ? ? 1.271 32.800 ? 1307 100.000 18 1 3.270 4.130 ? ? ? 0.027 ? ? 0.818 31.900 ? 1337 100.000 19 1 4.130 50.000 ? ? ? 0.025 ? ? 0.690 32.100 ? 1367 99.300 20 1 # _refine.entry_id 4DB5 _refine.ls_d_res_high 1.5220 _refine.ls_d_res_low 29.1470 _refine.pdbx_ls_sigma_F 1.340 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 99.9800 _refine.ls_number_reflns_obs 26128 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ? _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1614 _refine.ls_R_factor_R_work 0.1606 _refine.ls_wR_factor_R_work ? _refine.ls_R_factor_R_free 0.1757 _refine.ls_wR_factor_R_free ? _refine.ls_percent_reflns_R_free 5.1000 _refine.ls_number_reflns_R_free 1333 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 16.9381 _refine.solvent_model_param_bsol 53.3620 _refine.solvent_model_param_ksol 0.4420 _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.0000 _refine.aniso_B[2][2] 0.0000 _refine.aniso_B[3][3] 0.0000 _refine.aniso_B[1][2] 0.0000 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] -0.0000 _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_ML 0.1600 _refine.overall_SU_B ? _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii 0.9800 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model 'pdb entry 3FC0' _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set 0.9095 _refine.B_iso_max 57.920 _refine.B_iso_min 7.420 _refine.pdbx_overall_phase_error 15.6300 _refine.occupancy_max 1.000 _refine.occupancy_min 0.210 _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_diffrn_id 1 _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _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 961 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 19 _refine_hist.number_atoms_solvent 122 _refine_hist.number_atoms_total 1102 _refine_hist.d_res_high 1.5220 _refine_hist.d_res_low 29.1470 # 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_restraint_function _refine_ls_restr.pdbx_refine_id f_bond_d 1101 0.007 ? ? ? 'X-RAY DIFFRACTION' f_angle_d 1508 1.171 ? ? ? 'X-RAY DIFFRACTION' f_chiral_restr 160 0.080 ? ? ? 'X-RAY DIFFRACTION' f_plane_restr 197 0.005 ? ? ? 'X-RAY DIFFRACTION' f_dihedral_angle_d 424 18.525 ? ? ? '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 1.5217 1.5760 10 100.0000 2477 . 0.1916 0.2516 . 144 . 2621 . . 'X-RAY DIFFRACTION' 1.5760 1.6391 10 100.0000 2461 . 0.1731 0.1848 . 124 . 2585 . . 'X-RAY DIFFRACTION' 1.6391 1.7137 10 100.0000 2465 . 0.1670 0.1974 . 124 . 2589 . . 'X-RAY DIFFRACTION' 1.7137 1.8041 10 100.0000 2424 . 0.1621 0.1721 . 157 . 2581 . . 'X-RAY DIFFRACTION' 1.8041 1.9171 10 100.0000 2482 . 0.1584 0.1860 . 133 . 2615 . . 'X-RAY DIFFRACTION' 1.9171 2.0651 10 100.0000 2452 . 0.1549 0.1691 . 118 . 2570 . . 'X-RAY DIFFRACTION' 2.0651 2.2728 10 100.0000 2480 . 0.1476 0.1817 . 129 . 2609 . . 'X-RAY DIFFRACTION' 2.2728 2.6015 10 100.0000 2480 . 0.1594 0.1830 . 139 . 2619 . . 'X-RAY DIFFRACTION' 2.6015 3.2769 10 100.0000 2489 . 0.1691 0.1602 . 146 . 2635 . . 'X-RAY DIFFRACTION' 3.2769 29.1519 10 100.0000 2585 . 0.1565 0.1657 . 119 . 2704 . . 'X-RAY DIFFRACTION' # _struct.entry_id 4DB5 _struct.title 'Crystal structure of Rabbit GITRL' _struct.pdbx_descriptor 'Tumor necrosis factor ligand superfamily member 18' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 4DB5 _struct_keywords.text ;GITRL, GLUCOCORTICOID-INDUCED TNF RECEPTOR LIGAND, IMMUNE SYSTEM, TNFRSF18, Structural genomics, PSI-Biology, New York Structural Genomics Research Consortium, NYSGRC, Atoms-to-Animals: The Immune Function Network, IFN ; _struct_keywords.pdbx_keywords 'IMMUNE SYSTEM' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details 'The biological assembly is a trimer generated from the monomer in the asymmetric unit by crystallographic symmetry operations' # 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 102 ? VAL A 106 ? SER A 102 VAL A 106 5 ? 5 HELX_P HELX_P2 2 LEU A 107 ? THR A 111 ? LEU A 107 THR A 111 5 ? 5 HELX_P HELX_P3 3 PRO A 121 ? SER A 125 ? PRO A 121 SER A 125 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_conn.id disulf1 _struct_conn.conn_type_id disulf _struct_conn.pdbx_leaving_atom_flag ? _struct_conn.pdbx_PDB_id ? _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 6 _struct_conn.ptnr1_label_atom_id SG _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 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 26 _struct_conn.ptnr2_label_atom_id SG _struct_conn.pdbx_ptnr2_label_alt_id ? _struct_conn.pdbx_ptnr2_PDB_ins_code ? _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 6 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 26 _struct_conn.ptnr2_symmetry 1_555 _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 2.024 _struct_conn.pdbx_value_order ? # _struct_conn_type.id disulf _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 GLY 11 A . ? GLY 11 A PRO 12 A ? PRO 12 A 1 -5.01 2 LEU 13 A . ? LEU 13 A PRO 14 A ? PRO 14 A 1 9.11 3 GLU 20 A . ? GLU 20 A PRO 21 A ? PRO 21 A 1 -2.46 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 5 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? anti-parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? anti-parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? 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 TRP A 17 ? GLU A 20 ? TRP A 17 GLU A 20 A 2 VAL A 7 ? PHE A 10 ? VAL A 7 PHE A 10 A 3 TYR A 112 ? VAL A 119 ? TYR A 112 VAL A 119 A 4 GLY A 41 ? VAL A 49 ? GLY A 41 VAL A 49 A 5 GLN A 82 ? PHE A 90 ? GLN A 82 PHE A 90 B 1 VAL A 27 ? SER A 31 ? VAL A 27 SER A 31 B 2 LYS A 34 ? ILE A 37 ? LYS A 34 ILE A 37 B 3 ILE A 95 ? PHE A 100 ? ILE A 95 PHE A 100 B 4 VAL A 63 ? LYS A 67 ? VAL A 63 LYS A 67 B 5 GLU A 70 ? LEU A 75 ? GLU A 70 LEU A 75 # 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 GLN A 18 ? O GLN A 18 N LYS A 9 ? N LYS A 9 A 2 3 N PHE A 10 ? N PHE A 10 O TRP A 113 ? O TRP A 113 A 3 4 O LEU A 118 ? O LEU A 118 N LEU A 42 ? N LEU A 42 A 4 5 N TYR A 43 ? N TYR A 43 O TYR A 88 ? O TYR A 88 B 1 2 N ASN A 28 ? N ASN A 28 O LYS A 36 ? O LYS A 36 B 2 3 N LEU A 35 ? N LEU A 35 O ILE A 96 ? O ILE A 96 B 3 4 O GLU A 97 ? O GLU A 97 N CYS A 66 ? N CYS A 66 B 4 5 N VAL A 63 ? N VAL A 63 O LEU A 75 ? O LEU A 75 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id ? _struct_site.pdbx_auth_comp_id ? _struct_site.pdbx_auth_seq_id ? _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 13 _struct_site.details 'BINDING SITE FOR RESIDUE B3P A 201' # 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 13 MET A 19 ? MET A 19 . ? 5_555 ? 2 AC1 13 GLU A 20 ? GLU A 20 . ? 5_555 ? 3 AC1 13 PRO A 22 ? PRO A 22 . ? 5_555 ? 4 AC1 13 ASN A 40 ? ASN A 40 . ? 1_555 ? 5 AC1 13 ASP A 91 ? ASP A 91 . ? 1_555 ? 6 AC1 13 GLN A 122 ? GLN A 122 . ? 2_555 ? 7 AC1 13 PHE A 123 ? PHE A 123 . ? 2_555 ? 8 AC1 13 SER A 125 ? SER A 125 . ? 1_555 ? 9 AC1 13 HOH C . ? HOH A 331 . ? 5_555 ? 10 AC1 13 HOH C . ? HOH A 365 . ? 1_555 ? 11 AC1 13 HOH C . ? HOH A 391 . ? 1_555 ? 12 AC1 13 HOH C . ? HOH A 421 . ? 1_555 ? 13 AC1 13 HOH C . ? HOH A 422 . ? 1_555 ? # _atom_sites.entry_id 4DB5 _atom_sites.fract_transf_matrix[1][1] 0.007871 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.007871 _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] 0.007871 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O S # 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 THR 1 1 ? ? ? A . n A 1 2 ALA 2 2 ? ? ? A . n A 1 3 LYS 3 3 ? ? ? A . n A 1 4 GLU 4 4 ? ? ? A . n A 1 5 ALA 5 5 5 ALA ALA A . n A 1 6 CYS 6 6 6 CYS CYS A . n A 1 7 VAL 7 7 7 VAL VAL A . n A 1 8 ALA 8 8 8 ALA ALA A . n A 1 9 LYS 9 9 9 LYS LYS A . n A 1 10 PHE 10 10 10 PHE PHE A . n A 1 11 GLY 11 11 11 GLY GLY A . n A 1 12 PRO 12 12 12 PRO PRO A . n A 1 13 LEU 13 13 13 LEU LEU A . n A 1 14 PRO 14 14 14 PRO PRO A . n A 1 15 SER 15 15 15 SER SER A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 TRP 17 17 17 TRP TRP A . n A 1 18 GLN 18 18 18 GLN GLN A . n A 1 19 MET 19 19 19 MET MET A . n A 1 20 GLU 20 20 20 GLU GLU A . n A 1 21 PRO 21 21 21 PRO PRO A . n A 1 22 PRO 22 22 22 PRO PRO A . n A 1 23 LYS 23 23 23 LYS LYS A . n A 1 24 PRO 24 24 24 PRO PRO A . n A 1 25 SER 25 25 25 SER SER A . n A 1 26 CYS 26 26 26 CYS CYS A . n A 1 27 VAL 27 27 27 VAL VAL A . n A 1 28 ASN 28 28 28 ASN ASN A . n A 1 29 LYS 29 29 29 LYS LYS A . n A 1 30 ILE 30 30 30 ILE ILE A . n A 1 31 SER 31 31 31 SER SER A . n A 1 32 ASP 32 32 32 ASP ASP A . n A 1 33 TRP 33 33 33 TRP TRP A . n A 1 34 LYS 34 34 34 LYS LYS A . n A 1 35 LEU 35 35 35 LEU LEU A . n A 1 36 LYS 36 36 36 LYS LYS A . n A 1 37 ILE 37 37 37 ILE ILE A . n A 1 38 LEU 38 38 38 LEU LEU A . n A 1 39 GLN 39 39 39 GLN GLN A . n A 1 40 ASN 40 40 40 ASN ASN A . n A 1 41 GLY 41 41 41 GLY GLY A . n A 1 42 LEU 42 42 42 LEU LEU A . n A 1 43 TYR 43 43 43 TYR TYR A . n A 1 44 ILE 44 44 44 ILE ILE A . n A 1 45 ILE 45 45 45 ILE ILE A . n A 1 46 TYR 46 46 46 TYR TYR A . n A 1 47 GLY 47 47 47 GLY GLY A . n A 1 48 GLN 48 48 48 GLN GLN A . n A 1 49 VAL 49 49 49 VAL VAL A . n A 1 50 ALA 50 50 50 ALA ALA A . n A 1 51 PRO 51 51 51 PRO PRO A . n A 1 52 ASP 52 52 52 ASP ASP A . n A 1 53 PRO 53 53 53 PRO PRO A . n A 1 54 THR 54 54 54 THR THR A . n A 1 55 TYR 55 55 55 TYR TYR A . n A 1 56 LYS 56 56 56 LYS LYS A . n A 1 57 GLY 57 57 57 GLY GLY A . n A 1 58 PHE 58 58 58 PHE PHE A . n A 1 59 ALA 59 59 59 ALA ALA A . n A 1 60 PRO 60 60 60 PRO PRO A . n A 1 61 PHE 61 61 61 PHE PHE A . n A 1 62 GLU 62 62 62 GLU GLU A . n A 1 63 VAL 63 63 63 VAL VAL A . n A 1 64 GLN 64 64 64 GLN GLN A . n A 1 65 LEU 65 65 65 LEU LEU A . n A 1 66 CYS 66 66 66 CYS CYS A . n A 1 67 LYS 67 67 67 LYS LYS A . n A 1 68 ASN 68 68 68 ASN ASN A . n A 1 69 LYS 69 69 69 LYS LYS A . n A 1 70 GLU 70 70 70 GLU GLU A . n A 1 71 ALA 71 71 71 ALA ALA A . n A 1 72 ILE 72 72 72 ILE ILE A . n A 1 73 GLN 73 73 73 GLN GLN A . n A 1 74 THR 74 74 74 THR THR A . n A 1 75 LEU 75 75 75 LEU LEU A . n A 1 76 THR 76 76 76 THR THR A . n A 1 77 ASN 77 77 77 ASN ASN A . n A 1 78 ASN 78 78 78 ASN ASN A . n A 1 79 SER 79 79 79 SER SER A . n A 1 80 LYS 80 80 80 LYS LYS A . n A 1 81 ILE 81 81 81 ILE ILE A . n A 1 82 GLN 82 82 82 GLN GLN A . n A 1 83 ASN 83 83 83 ASN ASN A . n A 1 84 LEU 84 84 84 LEU LEU A . n A 1 85 GLY 85 85 85 GLY GLY A . n A 1 86 GLY 86 86 86 GLY GLY A . n A 1 87 ILE 87 87 87 ILE ILE A . n A 1 88 TYR 88 88 88 TYR TYR A . n A 1 89 GLU 89 89 89 GLU GLU A . n A 1 90 PHE 90 90 90 PHE PHE A . n A 1 91 ASP 91 91 91 ASP ASP A . n A 1 92 ALA 92 92 92 ALA ALA A . n A 1 93 GLY 93 93 93 GLY GLY A . n A 1 94 ASP 94 94 94 ASP ASP A . n A 1 95 ILE 95 95 95 ILE ILE A . n A 1 96 ILE 96 96 96 ILE ILE A . n A 1 97 GLU 97 97 97 GLU GLU A . n A 1 98 LEU 98 98 98 LEU LEU A . n A 1 99 ARG 99 99 99 ARG ARG A . n A 1 100 PHE 100 100 100 PHE PHE A . n A 1 101 ASN 101 101 101 ASN ASN A . n A 1 102 SER 102 102 102 SER SER A . n A 1 103 ASP 103 103 103 ASP ASP A . n A 1 104 ASP 104 104 104 ASP ASP A . n A 1 105 GLN 105 105 105 GLN GLN A . n A 1 106 VAL 106 106 106 VAL VAL A . n A 1 107 LEU 107 107 107 LEU LEU A . n A 1 108 LYS 108 108 108 LYS LYS A . n A 1 109 ASN 109 109 109 ASN ASN A . n A 1 110 ASN 110 110 110 ASN ASN A . n A 1 111 THR 111 111 111 THR THR A . n A 1 112 TYR 112 112 112 TYR TYR A . n A 1 113 TRP 113 113 113 TRP TRP A . n A 1 114 GLY 114 114 114 GLY GLY A . n A 1 115 ILE 115 115 115 ILE ILE A . n A 1 116 VAL 116 116 116 VAL VAL A . n A 1 117 LEU 117 117 117 LEU LEU A . n A 1 118 LEU 118 118 118 LEU LEU A . n A 1 119 VAL 119 119 119 VAL VAL A . n A 1 120 THR 120 120 120 THR THR A . n A 1 121 PRO 121 121 121 PRO PRO A . n A 1 122 GLN 122 122 122 GLN GLN A . n A 1 123 PHE 123 123 123 PHE PHE A . n A 1 124 SER 124 124 124 SER SER A . n A 1 125 SER 125 125 125 SER SER A . n # loop_ _pdbx_SG_project.id _pdbx_SG_project.project_name _pdbx_SG_project.full_name_of_center _pdbx_SG_project.initial_of_center 1 PSI:Biology 'New York Structural Genomics Research Consortium' NYSGRC 2 PSI:Biology 'Atoms-to-Animals: The Immune Function Network' IFN # 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_and_software_defined_assembly PISA trimeric 3 2 software_defined_assembly PISA dodecameric 12 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2,3 A,B,C 2 1,2,3,4,5,6,7,8,9,10,11,12 A,B,C # 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)' 4110 ? 1 MORE -23 ? 1 'SSA (A^2)' 16900 ? 2 'ABSA (A^2)' 31390 ? 2 MORE -152 ? 2 'SSA (A^2)' 52660 ? # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 2 'crystal symmetry operation' 7_555 -z,-x,y 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 3 'crystal symmetry operation' 10_555 -y,z,-x 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 4 'crystal symmetry operation' 16_544 x,-y-1/2,-z-1/2 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 -63.5235000000 0.0000000000 0.0000000000 -1.0000000000 -63.5235000000 5 'crystal symmetry operation' 20_544 -z,x-1/2,-y-1/2 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 -63.5235000000 0.0000000000 -1.0000000000 0.0000000000 -63.5235000000 6 'crystal symmetry operation' 24_544 -y,-z-1/2,x-1/2 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -63.5235000000 1.0000000000 0.0000000000 0.0000000000 -63.5235000000 7 'crystal symmetry operation' 27_554 -x+1/2,y,-z-1/2 -1.0000000000 0.0000000000 0.0000000000 63.5235000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 -63.5235000000 8 'crystal symmetry operation' 30_554 z+1/2,-x,-y-1/2 0.0000000000 0.0000000000 1.0000000000 63.5235000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 -63.5235000000 9 'crystal symmetry operation' 33_554 y+1/2,z,x-1/2 0.0000000000 1.0000000000 0.0000000000 63.5235000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 -63.5235000000 10 'crystal symmetry operation' 38_545 -x+1/2,-y-1/2,z -1.0000000000 0.0000000000 0.0000000000 63.5235000000 0.0000000000 -1.0000000000 0.0000000000 -63.5235000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 11 'crystal symmetry operation' 41_545 z+1/2,x-1/2,y 0.0000000000 0.0000000000 1.0000000000 63.5235000000 1.0000000000 0.0000000000 0.0000000000 -63.5235000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 12 'crystal symmetry operation' 47_545 y+1/2,-z-1/2,-x 0.0000000000 1.0000000000 0.0000000000 63.5235000000 0.0000000000 0.0000000000 -1.0000000000 -63.5235000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A HOH 303 ? C HOH . 2 1 A HOH 404 ? C HOH . 3 1 A HOH 405 ? C HOH . # 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 2012-03-21 2 'Structure model' 1 1 2012-06-06 # _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_group.ordinal 1 _pdbx_audit_revision_group.revision_ordinal 2 _pdbx_audit_revision_group.data_content_type 'Structure model' _pdbx_audit_revision_group.group 'Structure summary' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined -2.9821 -22.5775 -11.6534 0.0770 0.1121 0.1559 0.0008 0.0572 0.0070 2.9317 1.7549 3.5404 -0.3997 -0.3154 0.4299 0.0895 -0.0251 -0.0367 -0.0362 0.1924 0.4175 0.0648 -0.2407 -0.2396 'X-RAY DIFFRACTION' 2 ? refined 7.2813 -26.2788 -21.6007 0.0738 0.0741 0.0902 0.0167 0.0026 -0.0071 0.3186 2.1304 0.6206 -0.0502 0.1161 0.1728 0.0271 0.0263 -0.0486 0.0215 0.0198 0.0204 0.0178 0.0389 -0.0191 'X-RAY DIFFRACTION' 3 ? refined 4.1322 -21.8708 -20.6955 0.0458 0.0894 0.1076 0.0035 0.0280 -0.0038 0.9396 4.0802 0.6721 -1.4459 0.0848 0.0905 0.0594 -0.0098 -0.0546 0.0304 0.0071 0.0859 -0.1803 -0.0468 -0.0444 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 5 A 26 ;chain 'A' and (resseq 5:26) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 2 2 A 27 A 90 ;chain 'A' and (resseq 27:90) ; ? ? ? ? ? 'X-RAY DIFFRACTION' 3 3 A 91 A 125 ;chain 'A' and (resseq 91:125) ; ? ? ? ? ? # 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 SCALEPACK . ? program 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 2 PHENIX 1.7.3_928 ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 3 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 CBASS . ? ? ? ? 'data collection' ? ? ? 5 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 6 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? 7 PHENIX 1.7.3_928 ? ? ? ? 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 ILE 87 ? ? O A HOH 322 ? ? 2.17 2 1 O A HOH 421 ? ? O A HOH 422 ? ? 2.17 3 1 OD1 A ASN 28 ? A O A HOH 319 ? ? 2.18 # loop_ _pdbx_validate_symm_contact.id _pdbx_validate_symm_contact.PDB_model_num _pdbx_validate_symm_contact.auth_atom_id_1 _pdbx_validate_symm_contact.auth_asym_id_1 _pdbx_validate_symm_contact.auth_comp_id_1 _pdbx_validate_symm_contact.auth_seq_id_1 _pdbx_validate_symm_contact.PDB_ins_code_1 _pdbx_validate_symm_contact.label_alt_id_1 _pdbx_validate_symm_contact.site_symmetry_1 _pdbx_validate_symm_contact.auth_atom_id_2 _pdbx_validate_symm_contact.auth_asym_id_2 _pdbx_validate_symm_contact.auth_comp_id_2 _pdbx_validate_symm_contact.auth_seq_id_2 _pdbx_validate_symm_contact.PDB_ins_code_2 _pdbx_validate_symm_contact.label_alt_id_2 _pdbx_validate_symm_contact.site_symmetry_2 _pdbx_validate_symm_contact.dist 1 1 O A HOH 374 ? ? 1_555 O A HOH 402 ? ? 10_555 2.12 2 1 O A HOH 356 ? ? 1_555 O A HOH 402 ? ? 10_555 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 LYS A 16 ? ? -105.89 -130.56 2 1 TRP A 33 ? ? 72.52 -0.31 3 1 ASN A 110 ? ? -141.36 24.18 4 1 THR A 120 ? ? -118.58 73.05 # 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 THR 1 ? A THR 1 2 1 Y 1 A ALA 2 ? A ALA 2 3 1 Y 1 A LYS 3 ? A LYS 3 4 1 Y 1 A GLU 4 ? A GLU 4 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 '2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL' B3P 3 water HOH # 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 B3P 1 201 1 B3P B3P A . C 3 HOH 1 301 1 HOH HOH A . C 3 HOH 2 302 2 HOH HOH A . C 3 HOH 3 303 3 HOH HOH A . C 3 HOH 4 304 4 HOH HOH A . C 3 HOH 5 305 5 HOH HOH A . C 3 HOH 6 306 6 HOH HOH A . C 3 HOH 7 307 7 HOH HOH A . C 3 HOH 8 308 8 HOH HOH A . C 3 HOH 9 309 9 HOH HOH A . C 3 HOH 10 310 10 HOH HOH A . C 3 HOH 11 311 11 HOH HOH A . C 3 HOH 12 312 12 HOH HOH A . C 3 HOH 13 313 13 HOH HOH A . C 3 HOH 14 314 14 HOH HOH A . C 3 HOH 15 315 15 HOH HOH A . C 3 HOH 16 316 16 HOH HOH A . C 3 HOH 17 317 17 HOH HOH A . C 3 HOH 18 318 18 HOH HOH A . C 3 HOH 19 319 19 HOH HOH A . C 3 HOH 20 320 21 HOH HOH A . C 3 HOH 21 321 22 HOH HOH A . C 3 HOH 22 322 23 HOH HOH A . C 3 HOH 23 323 24 HOH HOH A . C 3 HOH 24 324 25 HOH HOH A . C 3 HOH 25 325 26 HOH HOH A . C 3 HOH 26 326 27 HOH HOH A . C 3 HOH 27 327 28 HOH HOH A . C 3 HOH 28 328 29 HOH HOH A . C 3 HOH 29 329 30 HOH HOH A . C 3 HOH 30 330 31 HOH HOH A . C 3 HOH 31 331 32 HOH HOH A . C 3 HOH 32 332 33 HOH HOH A . C 3 HOH 33 333 34 HOH HOH A . C 3 HOH 34 334 35 HOH HOH A . C 3 HOH 35 335 36 HOH HOH A . C 3 HOH 36 336 37 HOH HOH A . C 3 HOH 37 337 38 HOH HOH A . C 3 HOH 38 338 39 HOH HOH A . C 3 HOH 39 339 40 HOH HOH A . C 3 HOH 40 340 41 HOH HOH A . C 3 HOH 41 341 43 HOH HOH A . C 3 HOH 42 342 44 HOH HOH A . C 3 HOH 43 343 45 HOH HOH A . C 3 HOH 44 344 46 HOH HOH A . C 3 HOH 45 345 48 HOH HOH A . C 3 HOH 46 346 49 HOH HOH A . C 3 HOH 47 347 50 HOH HOH A . C 3 HOH 48 348 51 HOH HOH A . C 3 HOH 49 349 52 HOH HOH A . C 3 HOH 50 350 53 HOH HOH A . C 3 HOH 51 351 54 HOH HOH A . C 3 HOH 52 352 55 HOH HOH A . C 3 HOH 53 353 56 HOH HOH A . C 3 HOH 54 354 57 HOH HOH A . C 3 HOH 55 355 59 HOH HOH A . C 3 HOH 56 356 60 HOH HOH A . C 3 HOH 57 357 61 HOH HOH A . C 3 HOH 58 358 62 HOH HOH A . C 3 HOH 59 359 63 HOH HOH A . C 3 HOH 60 360 64 HOH HOH A . C 3 HOH 61 361 65 HOH HOH A . C 3 HOH 62 362 66 HOH HOH A . C 3 HOH 63 363 67 HOH HOH A . C 3 HOH 64 364 68 HOH HOH A . C 3 HOH 65 365 69 HOH HOH A . C 3 HOH 66 366 70 HOH HOH A . C 3 HOH 67 367 71 HOH HOH A . C 3 HOH 68 368 72 HOH HOH A . C 3 HOH 69 369 73 HOH HOH A . C 3 HOH 70 370 75 HOH HOH A . C 3 HOH 71 371 76 HOH HOH A . C 3 HOH 72 372 77 HOH HOH A . C 3 HOH 73 373 79 HOH HOH A . C 3 HOH 74 374 80 HOH HOH A . C 3 HOH 75 375 81 HOH HOH A . C 3 HOH 76 376 83 HOH HOH A . C 3 HOH 77 377 84 HOH HOH A . C 3 HOH 78 378 85 HOH HOH A . C 3 HOH 79 379 86 HOH HOH A . C 3 HOH 80 380 87 HOH HOH A . C 3 HOH 81 381 88 HOH HOH A . C 3 HOH 82 382 89 HOH HOH A . C 3 HOH 83 383 90 HOH HOH A . C 3 HOH 84 384 91 HOH HOH A . C 3 HOH 85 385 92 HOH HOH A . C 3 HOH 86 386 94 HOH HOH A . C 3 HOH 87 387 95 HOH HOH A . C 3 HOH 88 388 96 HOH HOH A . C 3 HOH 89 389 97 HOH HOH A . C 3 HOH 90 390 98 HOH HOH A . C 3 HOH 91 391 99 HOH HOH A . C 3 HOH 92 392 102 HOH HOH A . C 3 HOH 93 393 103 HOH HOH A . C 3 HOH 94 394 104 HOH HOH A . C 3 HOH 95 395 105 HOH HOH A . C 3 HOH 96 396 106 HOH HOH A . C 3 HOH 97 397 107 HOH HOH A . C 3 HOH 98 398 108 HOH HOH A . C 3 HOH 99 399 109 HOH HOH A . C 3 HOH 100 400 110 HOH HOH A . C 3 HOH 101 401 111 HOH HOH A . C 3 HOH 102 402 112 HOH HOH A . C 3 HOH 103 403 113 HOH HOH A . C 3 HOH 104 404 404 HOH HOH A . C 3 HOH 105 405 115 HOH HOH A . C 3 HOH 106 406 117 HOH HOH A . C 3 HOH 107 407 118 HOH HOH A . C 3 HOH 108 408 119 HOH HOH A . C 3 HOH 109 409 121 HOH HOH A . C 3 HOH 110 410 122 HOH HOH A . C 3 HOH 111 411 123 HOH HOH A . C 3 HOH 112 412 124 HOH HOH A . C 3 HOH 113 413 126 HOH HOH A . C 3 HOH 114 414 129 HOH HOH A . C 3 HOH 115 415 132 HOH HOH A . C 3 HOH 116 416 133 HOH HOH A . C 3 HOH 117 417 134 HOH HOH A . C 3 HOH 118 418 135 HOH HOH A . C 3 HOH 119 419 137 HOH HOH A . C 3 HOH 120 420 140 HOH HOH A . C 3 HOH 121 421 141 HOH HOH A . C 3 HOH 122 422 142 HOH HOH A . #