data_3H6N # _entry.id 3H6N # _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 3H6N RCSB RCSB052758 WWPDB D_1000052758 # _pdbx_database_status.entry_id 3H6N _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2009-04-23 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _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 'Tong, Y.' 1 'Nedyalkova, L.' 2 'Tempel, W.' 3 'MacKenzie, F.' 4 'Arrowsmith, C.H.' 5 'Edwards, A.M.' 6 'Bountra, C.' 7 'Weigelt, J.' 8 'Bochkarev, A.' 9 'Buck, M.' 10 'Park, H.' 11 'Structural Genomics Consortium (SGC)' 12 # _citation.id primary _citation.title 'Crystal Structure of the ubiquitin-like domain of plexin D1' _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 'Tong, Y.' 1 primary 'Nedyalkova, L.' 2 primary 'Tempel, W.' 3 primary 'MacKenzie, F.' 4 primary 'Arrowsmith, C.H.' 5 primary 'Edwards, A.M.' 6 primary 'Bountra, C.' 7 primary 'Weigelt, J.' 8 primary 'Bochkarev, A.' 9 primary 'Buck, M.' 10 primary 'Park, H.' 11 # _cell.entry_id 3H6N _cell.length_a 81.777 _cell.length_b 27.051 _cell.length_c 52.653 _cell.angle_alpha 90.00 _cell.angle_beta 114.06 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3H6N _symmetry.space_group_name_H-M 'C 1 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 # 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 Plexin-D1 14516.962 1 ? ? 'ubiquitin-like domain (UNP residues 1553-1678)' ? 2 non-polymer syn ARSENIC 74.922 2 ? ? ? ? 3 non-polymer syn 'UNKNOWN ATOM OR ION' ? 1 ? ? ? ? 4 water nat water 18.015 11 ? ? ? ? # _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 ;GAKPRNLNVSFQGCG(MSE)DSLSVRA(MSE)DTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDL DDTSVVEDGRKKLNTLAHYKIPEGASLA(MSE)SLIDKKDNTLGRVKDLDTEKYFHLVL ; _entity_poly.pdbx_seq_one_letter_code_can ;GAKPRNLNVSFQGCGMDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVED GRKKLNTLAHYKIPEGASLAMSLIDKKDNTLGRVKDLDTEKYFHLVL ; _entity_poly.pdbx_strand_id A _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 GLY n 1 2 ALA n 1 3 LYS n 1 4 PRO n 1 5 ARG n 1 6 ASN n 1 7 LEU n 1 8 ASN n 1 9 VAL n 1 10 SER n 1 11 PHE n 1 12 GLN n 1 13 GLY n 1 14 CYS n 1 15 GLY n 1 16 MSE n 1 17 ASP n 1 18 SER n 1 19 LEU n 1 20 SER n 1 21 VAL n 1 22 ARG n 1 23 ALA n 1 24 MSE n 1 25 ASP n 1 26 THR n 1 27 ASP n 1 28 THR n 1 29 LEU n 1 30 THR n 1 31 GLN n 1 32 VAL n 1 33 LYS n 1 34 GLU n 1 35 LYS n 1 36 ILE n 1 37 LEU n 1 38 GLU n 1 39 ALA n 1 40 PHE n 1 41 CYS n 1 42 LYS n 1 43 ASN n 1 44 VAL n 1 45 PRO n 1 46 TYR n 1 47 SER n 1 48 GLN n 1 49 TRP n 1 50 PRO n 1 51 ARG n 1 52 ALA n 1 53 GLU n 1 54 ASP n 1 55 VAL n 1 56 ASP n 1 57 LEU n 1 58 GLU n 1 59 TRP n 1 60 PHE n 1 61 ALA n 1 62 SER n 1 63 SER n 1 64 THR n 1 65 GLN n 1 66 SER n 1 67 TYR n 1 68 ILE n 1 69 LEU n 1 70 ARG n 1 71 ASP n 1 72 LEU n 1 73 ASP n 1 74 ASP n 1 75 THR n 1 76 SER n 1 77 VAL n 1 78 VAL n 1 79 GLU n 1 80 ASP n 1 81 GLY n 1 82 ARG n 1 83 LYS n 1 84 LYS n 1 85 LEU n 1 86 ASN n 1 87 THR n 1 88 LEU n 1 89 ALA n 1 90 HIS n 1 91 TYR n 1 92 LYS n 1 93 ILE n 1 94 PRO n 1 95 GLU n 1 96 GLY n 1 97 ALA n 1 98 SER n 1 99 LEU n 1 100 ALA n 1 101 MSE n 1 102 SER n 1 103 LEU n 1 104 ILE n 1 105 ASP n 1 106 LYS n 1 107 LYS n 1 108 ASP n 1 109 ASN n 1 110 THR n 1 111 LEU n 1 112 GLY n 1 113 ARG n 1 114 VAL n 1 115 LYS n 1 116 ASP n 1 117 LEU n 1 118 ASP n 1 119 THR n 1 120 GLU n 1 121 LYS n 1 122 TYR n 1 123 PHE n 1 124 HIS n 1 125 LEU n 1 126 VAL n 1 127 LEU 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 human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'PLXND1, KIAA0620' _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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)-V2R-pRARE2' _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name pET28-mhl _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code PLXD1_HUMAN _struct_ref.pdbx_db_accession Q9Y4D7 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;AKPRNLNVSFQGCGMDSLSVRAMDTDTLTQVKEKILEAFCKNVPYSQWPRAEDVDLEWFASSTQSYILRDLDDTSVVEDG RKKLNTLAHYKIPEGASLAMSLIDKKDNTLGRVKDLDTEKYFHLVL ; _struct_ref.pdbx_align_begin 1553 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3H6N _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 127 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9Y4D7 _struct_ref_seq.db_align_beg 1553 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 1678 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 1553 _struct_ref_seq.pdbx_auth_seq_align_end 1678 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3H6N _struct_ref_seq_dif.mon_id GLY _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q9Y4D7 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'EXPRESSION TAG' _struct_ref_seq_dif.pdbx_auth_seq_num 1552 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ARS non-polymer . ARSENIC ? As 74.922 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 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 UNX non-polymer . 'UNKNOWN ATOM OR ION' ? ? ? VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 3H6N _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_percent_sol 46.3 _exptl_crystal.density_Matthews 2.3 _exptl_crystal.density_meas ? _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 5.2 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details ;1.39M sodium citrate, 0.1M sodium cacodylate. The protein stock solution was adjusted to contain 15 mM TCEP, supplemented with 1:100 (w/w) chymotrypsin, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K ; _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_pH_range ? # _diffrn.id 1 _diffrn.ambient_temp ? _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 2009-03-18 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator ? _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 0.97942 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 19-ID' _diffrn_source.pdbx_wavelength_list 0.97942 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 19-ID # _reflns.entry_id 3H6N _reflns.d_resolution_high 2.000 _reflns.d_resolution_low 30.000 _reflns.number_obs 7245 _reflns.pdbx_Rmerge_I_obs 0.086 _reflns.pdbx_netI_over_sigmaI 9.600 _reflns.pdbx_chi_squared 2.407 _reflns.pdbx_redundancy 4.400 _reflns.percent_possible_obs 99.500 _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 _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 2.00 2.03 ? ? ? 0.499 ? ? 1.340 3.60 ? 381 99.70 ? 1 2.03 2.07 ? ? ? 0.553 ? ? 2.671 3.60 ? 343 99.40 ? 2 2.07 2.11 ? ? ? 0.446 ? ? 1.210 4.10 ? 357 100.00 ? 3 2.11 2.15 ? ? ? 0.416 ? ? 1.252 4.20 ? 356 99.70 ? 4 2.15 2.20 ? ? ? 0.329 ? ? 1.173 4.40 ? 365 100.00 ? 5 2.20 2.25 ? ? ? 0.383 ? ? 1.440 4.40 ? 355 98.30 ? 6 2.25 2.31 ? ? ? 0.300 ? ? 1.597 4.60 ? 333 100.00 ? 7 2.31 2.37 ? ? ? 0.281 ? ? 1.247 4.70 ? 378 100.00 ? 8 2.37 2.44 ? ? ? 0.208 ? ? 1.173 4.70 ? 363 100.00 ? 9 2.44 2.52 ? ? ? 0.191 ? ? 1.466 4.70 ? 360 99.70 ? 10 2.52 2.61 ? ? ? 0.173 ? ? 1.411 4.80 ? 353 100.00 ? 11 2.61 2.71 ? ? ? 0.144 ? ? 1.524 4.70 ? 376 99.70 ? 12 2.71 2.84 ? ? ? 0.119 ? ? 1.824 4.80 ? 348 100.00 ? 13 2.84 2.99 ? ? ? 0.102 ? ? 2.051 4.70 ? 364 99.70 ? 14 2.99 3.17 ? ? ? 0.094 ? ? 2.362 4.60 ? 353 100.00 ? 15 3.17 3.42 ? ? ? 0.069 ? ? 2.534 4.60 ? 371 99.20 ? 16 3.42 3.76 ? ? ? 0.068 ? ? 3.242 4.60 ? 366 98.70 ? 17 3.76 4.31 ? ? ? 0.063 ? ? 4.200 4.40 ? 356 98.10 ? 18 4.31 5.42 ? ? ? 0.055 ? ? 4.443 4.20 ? 383 99.20 ? 19 5.42 30.00 ? ? ? 0.069 ? ? 10.945 3.90 ? 384 98.50 ? 20 # _refine.entry_id 3H6N _refine.ls_d_res_high 2.004 _refine.ls_d_res_low 30.000 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 98.865 _refine.ls_number_reflns_obs 7229 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED. Phenix, Arp/warp, Coot and Molprobity were also used during refinement. ; _refine.ls_R_factor_obs 0.244 _refine.ls_R_factor_R_work 0.243 _refine.ls_wR_factor_R_work 0.239 _refine.ls_R_factor_R_free 0.276 _refine.ls_wR_factor_R_free 0.270 _refine.ls_percent_reflns_R_free 4.662 _refine.ls_number_reflns_R_free 337 _refine.B_iso_mean 31.154 _refine.aniso_B[1][1] -1.706 _refine.aniso_B[2][2] 1.444 _refine.aniso_B[3][3] 0.046 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] -0.265 _refine.aniso_B[2][3] 0.000 _refine.correlation_coeff_Fo_to_Fc 0.935 _refine.correlation_coeff_Fo_to_Fc_free 0.887 _refine.pdbx_overall_ESU_R 0.228 _refine.pdbx_overall_ESU_R_Free 0.191 _refine.overall_SU_ML 0.154 _refine.overall_SU_B 11.569 _refine.solvent_model_details 'MASK BULK SOLVENT' _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_ls_sigma_I ? _refine.ls_number_reflns_all ? _refine.ls_R_factor_all ? _refine.ls_redundancy_reflns_obs ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_starting_model ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.occupancy_max ? _refine.occupancy_min ? _refine.pdbx_isotropic_thermal_model ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 775 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 3 _refine_hist.number_atoms_solvent 11 _refine_hist.number_atoms_total 789 _refine_hist.d_res_high 2.004 _refine_hist.d_res_low 30.000 # loop_ _refine_ls_restr.type _refine_ls_restr.number _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 789 0.012 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 506 0.002 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1075 1.095 1.960 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1237 0.748 3.003 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 103 6.012 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 32 33.446 24.688 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 122 14.389 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 4 20.348 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 126 0.062 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 892 0.004 0.021 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 154 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 519 0.983 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 207 0.217 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 825 1.651 3.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 270 1.305 2.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 250 1.814 3.000 ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_low _refine_ls_shell.d_res_high _refine_ls_shell.number_reflns_all _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free _refine_ls_shell.number_reflns_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.R_factor_all _refine_ls_shell.pdbx_refine_id 20 2.056 2.004 559 93.560 505 0.349 18 0.290 . . . . . 'X-RAY DIFFRACTION' 20 2.112 2.056 495 99.394 469 0.322 23 0.264 . . . . . 'X-RAY DIFFRACTION' 20 2.173 2.112 493 99.594 470 0.301 21 0.251 . . . . . 'X-RAY DIFFRACTION' 20 2.239 2.173 497 98.793 470 0.294 21 0.365 . . . . . 'X-RAY DIFFRACTION' 20 2.312 2.239 468 98.932 440 0.280 23 0.434 . . . . . 'X-RAY DIFFRACTION' 20 2.393 2.312 462 99.784 445 0.262 16 0.291 . . . . . 'X-RAY DIFFRACTION' 20 2.483 2.393 451 99.557 429 0.236 20 0.190 . . . . . 'X-RAY DIFFRACTION' 20 2.583 2.483 419 99.523 399 0.263 18 0.229 . . . . . 'X-RAY DIFFRACTION' 20 2.697 2.583 425 99.765 406 0.264 18 0.161 . . . . . 'X-RAY DIFFRACTION' 20 2.828 2.697 383 100.000 361 0.275 22 0.271 . . . . . 'X-RAY DIFFRACTION' 20 2.979 2.828 386 99.741 365 0.262 20 0.305 . . . . . 'X-RAY DIFFRACTION' 20 3.158 2.979 360 100.000 336 0.268 24 0.300 . . . . . 'X-RAY DIFFRACTION' 20 3.374 3.158 333 99.099 317 0.243 13 0.271 . . . . . 'X-RAY DIFFRACTION' 20 3.640 3.374 305 99.016 289 0.229 13 0.184 . . . . . 'X-RAY DIFFRACTION' 20 3.982 3.640 295 98.305 272 0.190 18 0.298 . . . . . 'X-RAY DIFFRACTION' 20 4.442 3.982 276 98.188 258 0.189 13 0.281 . . . . . 'X-RAY DIFFRACTION' 20 5.110 4.442 228 99.123 214 0.176 12 0.284 . . . . . 'X-RAY DIFFRACTION' 20 6.214 5.110 205 99.512 190 0.214 14 0.236 . . . . . 'X-RAY DIFFRACTION' 20 8.605 6.214 170 98.824 163 0.278 5 0.364 . . . . . 'X-RAY DIFFRACTION' 20 30.000 8.605 102 97.059 94 0.305 5 0.453 . . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 3H6N _struct.title 'Crystal Structure of the ubiquitin-like domain of plexin D1' _struct.pdbx_descriptor Plexin-D1 _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3H6N _struct_keywords.text ;structural genomics consortium, SGC, MEMBRANE, transmembrane, receptor, Alternative splicing, Cell membrane, Glycoprotein, Polymorphism, SIGNALING PROTEIN ; _struct_keywords.pdbx_keywords 'SIGNALING 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 2 ? C N N 2 ? D N N 3 ? E N N 4 ? # _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 THR A 28 ? CYS A 41 ? THR A 1579 CYS A 1592 1 ? 14 HELX_P HELX_P2 2 PRO A 45 ? TRP A 49 ? PRO A 1596 TRP A 1600 5 ? 5 HELX_P HELX_P3 3 ARG A 51 ? GLU A 53 ? ARG A 1602 GLU A 1604 5 ? 3 # _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 GLY 15 C ? ? ? 1_555 A MSE 16 N ? ? A GLY 1566 A MSE 1567 1_555 ? ? ? ? ? ? ? 1.333 ? covale2 covale ? ? A MSE 16 C ? ? ? 1_555 A ASP 17 N ? ? A MSE 1567 A ASP 1568 1_555 ? ? ? ? ? ? ? 1.330 ? covale3 covale ? ? A ALA 23 C ? ? ? 1_555 A MSE 24 N ? ? A ALA 1574 A MSE 1575 1_555 ? ? ? ? ? ? ? 1.327 ? covale4 covale ? ? A MSE 24 C ? ? ? 1_555 A ASP 25 N ? ? A MSE 1575 A ASP 1576 1_555 ? ? ? ? ? ? ? 1.339 ? covale5 covale ? ? A ALA 100 C ? ? ? 1_555 A MSE 101 N ? ? A ALA 1651 A MSE 1652 1_555 ? ? ? ? ? ? ? 1.330 ? covale6 covale ? ? A MSE 101 C ? ? ? 1_555 A SER 102 N ? ? A MSE 1652 A SER 1653 1_555 ? ? ? ? ? ? ? 1.338 ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 5 ? B ? 2 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? anti-parallel A 2 3 ? parallel A 3 4 ? anti-parallel A 4 5 ? anti-parallel B 1 2 ? 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 LEU A 19 ? MSE A 24 ? LEU A 1570 MSE A 1575 A 2 PRO A 4 ? GLN A 12 ? PRO A 1555 GLN A 1563 A 3 SER A 98 ? LEU A 103 ? SER A 1649 LEU A 1654 A 4 VAL A 55 ? PHE A 60 ? VAL A 1606 PHE A 1611 A 5 SER A 66 ? ILE A 68 ? SER A 1617 ILE A 1619 B 1 VAL A 78 ? GLU A 79 ? VAL A 1629 GLU A 1630 B 2 ARG A 82 ? LYS A 83 ? ARG A 1633 LYS A 1634 # 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 ALA A 23 ? O ALA A 1574 N ARG A 5 ? N ARG A 1556 A 2 3 N SER A 10 ? N SER A 1561 O MSE A 101 ? O MSE A 1652 A 3 4 O ALA A 100 ? O ALA A 1651 N GLU A 58 ? N GLU A 1609 A 4 5 N TRP A 59 ? N TRP A 1610 O TYR A 67 ? O TYR A 1618 B 1 2 N GLU A 79 ? N GLU A 1630 O ARG A 82 ? O ARG A 1633 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE ARS A 1' AC2 Software ? ? ? ? 1 'BINDING SITE FOR RESIDUE ARS A 2' # 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 1 CYS A 41 ? CYS A 1592 . ? 1_555 ? 2 AC2 1 CYS A 14 ? CYS A 1565 . ? 1_555 ? # _atom_sites.entry_id 3H6N _atom_sites.fract_transf_matrix[1][1] 0.012228 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.005460 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.036967 _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] 0.020799 _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 AS C N O S SE X # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 1552 ? ? ? A . n A 1 2 ALA 2 1553 1553 ALA ALA A . n A 1 3 LYS 3 1554 1554 LYS LYS A . n A 1 4 PRO 4 1555 1555 PRO PRO A . n A 1 5 ARG 5 1556 1556 ARG ARG A . n A 1 6 ASN 6 1557 1557 ASN ASN A . n A 1 7 LEU 7 1558 1558 LEU LEU A . n A 1 8 ASN 8 1559 1559 ASN ASN A . n A 1 9 VAL 9 1560 1560 VAL VAL A . n A 1 10 SER 10 1561 1561 SER SER A . n A 1 11 PHE 11 1562 1562 PHE PHE A . n A 1 12 GLN 12 1563 1563 GLN GLN A . n A 1 13 GLY 13 1564 1564 GLY GLY A . n A 1 14 CYS 14 1565 1565 CYS CYS A . n A 1 15 GLY 15 1566 1566 GLY GLY A . n A 1 16 MSE 16 1567 1567 MSE MSE A . n A 1 17 ASP 17 1568 1568 ASP ASP A . n A 1 18 SER 18 1569 1569 SER SER A . n A 1 19 LEU 19 1570 1570 LEU LEU A . n A 1 20 SER 20 1571 1571 SER SER A . n A 1 21 VAL 21 1572 1572 VAL VAL A . n A 1 22 ARG 22 1573 1573 ARG ARG A . n A 1 23 ALA 23 1574 1574 ALA ALA A . n A 1 24 MSE 24 1575 1575 MSE MSE A . n A 1 25 ASP 25 1576 1576 ASP ASP A . n A 1 26 THR 26 1577 1577 THR THR A . n A 1 27 ASP 27 1578 1578 ASP ASP A . n A 1 28 THR 28 1579 1579 THR THR A . n A 1 29 LEU 29 1580 1580 LEU LEU A . n A 1 30 THR 30 1581 1581 THR THR A . n A 1 31 GLN 31 1582 1582 GLN GLN A . n A 1 32 VAL 32 1583 1583 VAL VAL A . n A 1 33 LYS 33 1584 1584 LYS LYS A . n A 1 34 GLU 34 1585 1585 GLU GLU A . n A 1 35 LYS 35 1586 1586 LYS LYS A . n A 1 36 ILE 36 1587 1587 ILE ILE A . n A 1 37 LEU 37 1588 1588 LEU LEU A . n A 1 38 GLU 38 1589 1589 GLU GLU A . n A 1 39 ALA 39 1590 1590 ALA ALA A . n A 1 40 PHE 40 1591 1591 PHE PHE A . n A 1 41 CYS 41 1592 1592 CYS CYS A . n A 1 42 LYS 42 1593 1593 LYS LYS A . n A 1 43 ASN 43 1594 1594 ASN ASN A . n A 1 44 VAL 44 1595 1595 VAL VAL A . n A 1 45 PRO 45 1596 1596 PRO PRO A . n A 1 46 TYR 46 1597 1597 TYR TYR A . n A 1 47 SER 47 1598 1598 SER SER A . n A 1 48 GLN 48 1599 1599 GLN GLN A . n A 1 49 TRP 49 1600 1600 TRP TRP A . n A 1 50 PRO 50 1601 1601 PRO PRO A . n A 1 51 ARG 51 1602 1602 ARG ARG A . n A 1 52 ALA 52 1603 1603 ALA ALA A . n A 1 53 GLU 53 1604 1604 GLU GLU A . n A 1 54 ASP 54 1605 1605 ASP ASP A . n A 1 55 VAL 55 1606 1606 VAL VAL A . n A 1 56 ASP 56 1607 1607 ASP ASP A . n A 1 57 LEU 57 1608 1608 LEU LEU A . n A 1 58 GLU 58 1609 1609 GLU GLU A . n A 1 59 TRP 59 1610 1610 TRP TRP A . n A 1 60 PHE 60 1611 1611 PHE PHE A . n A 1 61 ALA 61 1612 1612 ALA ALA A . n A 1 62 SER 62 1613 1613 SER SER A . n A 1 63 SER 63 1614 1614 SER SER A . n A 1 64 THR 64 1615 1615 THR THR A . n A 1 65 GLN 65 1616 1616 GLN GLN A . n A 1 66 SER 66 1617 1617 SER SER A . n A 1 67 TYR 67 1618 1618 TYR TYR A . n A 1 68 ILE 68 1619 1619 ILE ILE A . n A 1 69 LEU 69 1620 1620 LEU LEU A . n A 1 70 ARG 70 1621 1621 ARG ARG A . n A 1 71 ASP 71 1622 1622 ASP ASP A . n A 1 72 LEU 72 1623 1623 LEU LEU A . n A 1 73 ASP 73 1624 1624 ASP ASP A . n A 1 74 ASP 74 1625 1625 ASP ASP A . n A 1 75 THR 75 1626 1626 THR THR A . n A 1 76 SER 76 1627 1627 SER SER A . n A 1 77 VAL 77 1628 1628 VAL VAL A . n A 1 78 VAL 78 1629 1629 VAL VAL A . n A 1 79 GLU 79 1630 1630 GLU GLU A . n A 1 80 ASP 80 1631 1631 ASP ASP A . n A 1 81 GLY 81 1632 1632 GLY GLY A . n A 1 82 ARG 82 1633 1633 ARG ARG A . n A 1 83 LYS 83 1634 1634 LYS LYS A . n A 1 84 LYS 84 1635 1635 LYS LYS A . n A 1 85 LEU 85 1636 1636 LEU LEU A . n A 1 86 ASN 86 1637 1637 ASN ASN A . n A 1 87 THR 87 1638 1638 THR THR A . n A 1 88 LEU 88 1639 1639 LEU LEU A . n A 1 89 ALA 89 1640 1640 ALA ALA A . n A 1 90 HIS 90 1641 1641 HIS HIS A . n A 1 91 TYR 91 1642 1642 TYR TYR A . n A 1 92 LYS 92 1643 1643 LYS LYS A . n A 1 93 ILE 93 1644 1644 ILE ILE A . n A 1 94 PRO 94 1645 1645 PRO PRO A . n A 1 95 GLU 95 1646 1646 GLU GLU A . n A 1 96 GLY 96 1647 1647 GLY GLY A . n A 1 97 ALA 97 1648 1648 ALA ALA A . n A 1 98 SER 98 1649 1649 SER SER A . n A 1 99 LEU 99 1650 1650 LEU LEU A . n A 1 100 ALA 100 1651 1651 ALA ALA A . n A 1 101 MSE 101 1652 1652 MSE MSE A . n A 1 102 SER 102 1653 1653 SER SER A . n A 1 103 LEU 103 1654 1654 LEU LEU A . n A 1 104 ILE 104 1655 1655 ILE ILE A . n A 1 105 ASP 105 1656 1656 ASP ASP A . n A 1 106 LYS 106 1657 ? ? ? A . n A 1 107 LYS 107 1658 ? ? ? A . n A 1 108 ASP 108 1659 ? ? ? A . n A 1 109 ASN 109 1660 ? ? ? A . n A 1 110 THR 110 1661 ? ? ? A . n A 1 111 LEU 111 1662 ? ? ? A . n A 1 112 GLY 112 1663 ? ? ? A . n A 1 113 ARG 113 1664 ? ? ? A . n A 1 114 VAL 114 1665 ? ? ? A . n A 1 115 LYS 115 1666 ? ? ? A . n A 1 116 ASP 116 1667 ? ? ? A . n A 1 117 LEU 117 1668 ? ? ? A . n A 1 118 ASP 118 1669 ? ? ? A . n A 1 119 THR 119 1670 ? ? ? A . n A 1 120 GLU 120 1671 ? ? ? A . n A 1 121 LYS 121 1672 ? ? ? A . n A 1 122 TYR 122 1673 ? ? ? A . n A 1 123 PHE 123 1674 ? ? ? A . n A 1 124 HIS 124 1675 ? ? ? A . n A 1 125 LEU 125 1676 ? ? ? A . n A 1 126 VAL 126 1677 ? ? ? A . n A 1 127 LEU 127 1678 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'Structural Genomics Consortium' _pdbx_SG_project.initial_of_center SGC # 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 ARS 1 1 1 ARS ARS A . C 2 ARS 1 2 2 ARS ARS A . D 3 UNX 1 1679 1679 UNX UNX A . E 4 HOH 1 3 3 HOH HOH A . E 4 HOH 2 4 4 HOH HOH A . E 4 HOH 3 5 5 HOH HOH A . E 4 HOH 4 6 6 HOH HOH A . E 4 HOH 5 7 7 HOH HOH A . E 4 HOH 6 8 8 HOH HOH A . E 4 HOH 7 9 9 HOH HOH A . E 4 HOH 8 10 10 HOH HOH A . E 4 HOH 9 11 11 HOH HOH A . E 4 HOH 10 1680 1680 HOH HOH A . E 4 HOH 11 1681 1681 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 16 A MSE 1567 ? MET SELENOMETHIONINE 2 A MSE 24 A MSE 1575 ? MET SELENOMETHIONINE 3 A MSE 101 A MSE 1652 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E # 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)' 2120 ? 1 MORE -38 ? 1 'SSA (A^2)' 10890 ? # 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' 2_656 -x+1,y,-z+1 -1.0000000000 0.0000000000 0.0000000000 60.3107361298 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 48.0784559284 # 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 2009-05-19 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-11-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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 # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.contact_author' 3 3 'Structure model' '_software.contact_author_email' 4 3 'Structure model' '_software.date' 5 3 'Structure model' '_software.language' 6 3 'Structure model' '_software.location' 7 3 'Structure model' '_software.name' 8 3 'Structure model' '_software.type' 9 3 'Structure model' '_software.version' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 16.5258 _pdbx_refine_tls.origin_y 16.6552 _pdbx_refine_tls.origin_z 14.8903 _pdbx_refine_tls.T[1][1] 0.0439 _pdbx_refine_tls.T[2][2] 0.0751 _pdbx_refine_tls.T[3][3] 0.0843 _pdbx_refine_tls.T[1][2] -0.0152 _pdbx_refine_tls.T[1][3] 0.0303 _pdbx_refine_tls.T[2][3] -0.0101 _pdbx_refine_tls.L[1][1] 3.2374 _pdbx_refine_tls.L[2][2] 2.1422 _pdbx_refine_tls.L[3][3] 4.8958 _pdbx_refine_tls.L[1][2] 0.4764 _pdbx_refine_tls.L[1][3] 2.8561 _pdbx_refine_tls.L[2][3] 0.6545 _pdbx_refine_tls.S[1][1] -0.1521 _pdbx_refine_tls.S[2][2] 0.0831 _pdbx_refine_tls.S[3][3] 0.0690 _pdbx_refine_tls.S[1][2] -0.0408 _pdbx_refine_tls.S[1][3] -0.0478 _pdbx_refine_tls.S[2][3] 0.0034 _pdbx_refine_tls.S[2][1] -0.1307 _pdbx_refine_tls.S[3][1] 0.1086 _pdbx_refine_tls.S[3][2] -0.1199 _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' # _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 1656 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_seq_id 1553 _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.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.selection_details ? # _phasing.method SAD # loop_ _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id _software.pdbx_ordinal DENZO . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data reduction' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 1 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 2 SHELX . ? package 'George Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 3 DM . ? program 'K. Cowtan' ccp4@dl.ac.uk phasing http://www.ccp4.ac.uk/main.html Fortran_77 ? 4 REFMAC 5.5.0072 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 5 PDB_EXTRACT 3.005 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 # _pdbx_entry_details.entry_id 3H6N _pdbx_entry_details.sequence_details ;SOLVENT CONTENT AND MATTHEWS COEFFICIENT WERE CALCULATED BASED ON THE PURIFIED PROTEIN CONSTRUCT. HOWEVER, THE PROTEASE ADDED FOR CRYSTALLIZATION MAY HAVE REDUCED THE CHAIN LENGTH OF THE TARGET PROTEIN. ; _pdbx_entry_details.nonpolymer_details ;THE ELECTRON DENSITY SUGGESTS THE MODIFICATION OF THE SULFHYDRYL GROUPS OF CYS-1565 AND CYS-1592, POSSIBLY BY A REACTION INVOLVING CACODYLATE, SIMILAR TO SCOTT ET AL (1993, CHEM RES TOXICOL 6:102) AND GOLDGUR ET AL (1998, PROC NATL ACAD SCI USA 95:9150). ONLY THE PUTATIVE ARSENIC ATOMS OF THE MODIFICATION HAVE BEEN MODELED. ; _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? # loop_ _pdbx_unobs_or_zero_occ_atoms.id _pdbx_unobs_or_zero_occ_atoms.PDB_model_num _pdbx_unobs_or_zero_occ_atoms.polymer_flag _pdbx_unobs_or_zero_occ_atoms.occupancy_flag _pdbx_unobs_or_zero_occ_atoms.auth_asym_id _pdbx_unobs_or_zero_occ_atoms.auth_comp_id _pdbx_unobs_or_zero_occ_atoms.auth_seq_id _pdbx_unobs_or_zero_occ_atoms.PDB_ins_code _pdbx_unobs_or_zero_occ_atoms.auth_atom_id _pdbx_unobs_or_zero_occ_atoms.label_alt_id _pdbx_unobs_or_zero_occ_atoms.label_asym_id _pdbx_unobs_or_zero_occ_atoms.label_comp_id _pdbx_unobs_or_zero_occ_atoms.label_seq_id _pdbx_unobs_or_zero_occ_atoms.label_atom_id 1 1 Y 1 A LYS 1554 ? CG ? A LYS 3 CG 2 1 Y 1 A LYS 1554 ? CD ? A LYS 3 CD 3 1 Y 1 A LYS 1554 ? CE ? A LYS 3 CE 4 1 Y 1 A LYS 1554 ? NZ ? A LYS 3 NZ 5 1 Y 1 A LYS 1593 ? CD ? A LYS 42 CD 6 1 Y 1 A LYS 1593 ? CE ? A LYS 42 CE 7 1 Y 1 A LYS 1593 ? NZ ? A LYS 42 NZ 8 1 Y 1 A GLU 1604 ? CG ? A GLU 53 CG 9 1 Y 1 A GLU 1604 ? CD ? A GLU 53 CD 10 1 Y 1 A GLU 1604 ? OE1 ? A GLU 53 OE1 11 1 Y 1 A GLU 1604 ? OE2 ? A GLU 53 OE2 12 1 Y 1 A GLU 1609 ? CG ? A GLU 58 CG 13 1 Y 1 A GLU 1609 ? CD ? A GLU 58 CD 14 1 Y 1 A GLU 1609 ? OE1 ? A GLU 58 OE1 15 1 Y 1 A GLU 1609 ? OE2 ? A GLU 58 OE2 16 1 Y 1 A SER 1613 ? OG ? A SER 62 OG 17 1 Y 1 A SER 1614 ? OG ? A SER 63 OG 18 1 Y 1 A THR 1615 ? OG1 ? A THR 64 OG1 19 1 Y 1 A THR 1615 ? CG2 ? A THR 64 CG2 20 1 Y 1 A GLN 1616 ? CG ? A GLN 65 CG 21 1 Y 1 A GLN 1616 ? CD ? A GLN 65 CD 22 1 Y 1 A GLN 1616 ? OE1 ? A GLN 65 OE1 23 1 Y 1 A GLN 1616 ? NE2 ? A GLN 65 NE2 24 1 Y 1 A ARG 1621 ? CD ? A ARG 70 CD 25 1 Y 1 A ARG 1621 ? NE ? A ARG 70 NE 26 1 Y 1 A ARG 1621 ? CZ ? A ARG 70 CZ 27 1 Y 1 A ARG 1621 ? NH1 ? A ARG 70 NH1 28 1 Y 1 A ARG 1621 ? NH2 ? A ARG 70 NH2 29 1 Y 1 A VAL 1629 ? CG1 ? A VAL 78 CG1 30 1 Y 1 A VAL 1629 ? CG2 ? A VAL 78 CG2 31 1 Y 1 A GLU 1630 ? CG ? A GLU 79 CG 32 1 Y 1 A GLU 1630 ? CD ? A GLU 79 CD 33 1 Y 1 A GLU 1630 ? OE1 ? A GLU 79 OE1 34 1 Y 1 A GLU 1630 ? OE2 ? A GLU 79 OE2 35 1 Y 1 A ASP 1631 ? CG ? A ASP 80 CG 36 1 Y 1 A ASP 1631 ? OD1 ? A ASP 80 OD1 37 1 Y 1 A ASP 1631 ? OD2 ? A ASP 80 OD2 38 1 Y 1 A LYS 1635 ? CG ? A LYS 84 CG 39 1 Y 1 A LYS 1635 ? CD ? A LYS 84 CD 40 1 Y 1 A LYS 1635 ? CE ? A LYS 84 CE 41 1 Y 1 A LYS 1635 ? NZ ? A LYS 84 NZ 42 1 Y 1 A LYS 1643 ? CE ? A LYS 92 CE 43 1 Y 1 A LYS 1643 ? NZ ? A LYS 92 NZ # 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 GLY 1552 ? A GLY 1 2 1 Y 1 A LYS 1657 ? A LYS 106 3 1 Y 1 A LYS 1658 ? A LYS 107 4 1 Y 1 A ASP 1659 ? A ASP 108 5 1 Y 1 A ASN 1660 ? A ASN 109 6 1 Y 1 A THR 1661 ? A THR 110 7 1 Y 1 A LEU 1662 ? A LEU 111 8 1 Y 1 A GLY 1663 ? A GLY 112 9 1 Y 1 A ARG 1664 ? A ARG 113 10 1 Y 1 A VAL 1665 ? A VAL 114 11 1 Y 1 A LYS 1666 ? A LYS 115 12 1 Y 1 A ASP 1667 ? A ASP 116 13 1 Y 1 A LEU 1668 ? A LEU 117 14 1 Y 1 A ASP 1669 ? A ASP 118 15 1 Y 1 A THR 1670 ? A THR 119 16 1 Y 1 A GLU 1671 ? A GLU 120 17 1 Y 1 A LYS 1672 ? A LYS 121 18 1 Y 1 A TYR 1673 ? A TYR 122 19 1 Y 1 A PHE 1674 ? A PHE 123 20 1 Y 1 A HIS 1675 ? A HIS 124 21 1 Y 1 A LEU 1676 ? A LEU 125 22 1 Y 1 A VAL 1677 ? A VAL 126 23 1 Y 1 A LEU 1678 ? A LEU 127 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 ARSENIC ARS 3 'UNKNOWN ATOM OR ION' UNX 4 water HOH #