data_3DV6 # _entry.id 3DV6 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.329 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 3DV6 RCSB RCSB048528 WWPDB D_1000048528 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 3DUR . unspecified PDB 3DUS . unspecified PDB 3DUU . unspecified PDB 3DV4 . unspecified # _pdbx_database_status.entry_id 3DV6 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-07-18 _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.status_code_nmr_data ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Brooks, C.L.' 1 'Blackler, R.J.' 2 'Gerstenbruch, S.' 3 'Kosma, P.' 4 'Muller-Loennies, S.' 5 'Brade, H.' 6 'Evans, S.V.' 7 # _citation.id primary _citation.title 'Pseudo-symmetry and twinning in crystals of homologous antibody Fv fragments.' _citation.journal_abbrev 'Acta Crystallogr.,Sect.D' _citation.journal_volume 64 _citation.page_first 1250 _citation.page_last 1258 _citation.year 2008 _citation.journal_id_ASTM ABCRE6 _citation.country DK _citation.journal_id_ISSN 0907-4449 _citation.journal_id_CSD 0766 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 19018101 _citation.pdbx_database_id_DOI 10.1107/S0907444908033453 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Brooks, C.L.' 1 ? primary 'Blackler, R.J.' 2 ? primary 'Gerstenbruch, S.' 3 ? primary 'Kosma, P.' 4 ? primary 'Muller-Loennies, S.' 5 ? primary 'Brade, H.' 6 ? primary 'Evans, S.V.' 7 ? # _cell.length_a 71.420 _cell.length_b 71.420 _cell.length_c 85.080 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.entry_id 3DV6 _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 'P 43 21 2' _symmetry.entry_id 3DV6 _symmetry.Int_Tables_number 96 _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 'antibody Fv fragment SAG506-01' 12353.851 1 ? ? 'variable region fragment (Fv)' ? 2 polymer man 'Ig-like protein' 13442.986 1 ? ? ? ? 3 non-polymer syn 'MAGNESIUM ION' 24.305 2 ? ? ? ? 4 non-polymer man '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' 238.192 1 ? ? ? ? 5 non-polymer syn 'TETRAETHYLENE GLYCOL' 194.226 1 ? ? ? ? 6 water nat water 18.015 131 ? ? ? ? # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no ;DIVLTQSPSSLAVSAGERVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLT INGVQAEDLAVYYCKQSYNLRTFGGGTKLELK ; ;DIVLTQSPSSLAVSAGERVTMSCKSSQSLFKSRNQKNYLAWYQQKPGQSPKLLIYWASTRESGVPDRFTGSGSGTDFTLT INGVQAEDLAVYYCKQSYNLRTFGGGTKLELK ; A ? 2 'polypeptide(L)' no no ;EVKLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTVEYSASVKGRFTISRDNSQSI LYLQMNTLRAEDSATYYCARDGYYVDAMDYWGQGTSVTVSS ; ;EVKLVESGGGLVQPGGSLRLSCATSGFTFTDYYMSWVRQPPGKALEWLGFIRNKAKGYTVEYSASVKGRFTISRDNSQSI LYLQMNTLRAEDSATYYCARDGYYVDAMDYWGQGTSVTVSS ; B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 ASP n 1 2 ILE n 1 3 VAL n 1 4 LEU n 1 5 THR n 1 6 GLN n 1 7 SER n 1 8 PRO n 1 9 SER n 1 10 SER n 1 11 LEU n 1 12 ALA n 1 13 VAL n 1 14 SER n 1 15 ALA n 1 16 GLY n 1 17 GLU n 1 18 ARG n 1 19 VAL n 1 20 THR n 1 21 MET n 1 22 SER n 1 23 CYS n 1 24 LYS n 1 25 SER n 1 26 SER n 1 27 GLN n 1 28 SER n 1 29 LEU n 1 30 PHE n 1 31 LYS n 1 32 SER n 1 33 ARG n 1 34 ASN n 1 35 GLN n 1 36 LYS n 1 37 ASN n 1 38 TYR n 1 39 LEU n 1 40 ALA n 1 41 TRP n 1 42 TYR n 1 43 GLN n 1 44 GLN n 1 45 LYS n 1 46 PRO n 1 47 GLY n 1 48 GLN n 1 49 SER n 1 50 PRO n 1 51 LYS n 1 52 LEU n 1 53 LEU n 1 54 ILE n 1 55 TYR n 1 56 TRP n 1 57 ALA n 1 58 SER n 1 59 THR n 1 60 ARG n 1 61 GLU n 1 62 SER n 1 63 GLY n 1 64 VAL n 1 65 PRO n 1 66 ASP n 1 67 ARG n 1 68 PHE n 1 69 THR n 1 70 GLY n 1 71 SER n 1 72 GLY n 1 73 SER n 1 74 GLY n 1 75 THR n 1 76 ASP n 1 77 PHE n 1 78 THR n 1 79 LEU n 1 80 THR n 1 81 ILE n 1 82 ASN n 1 83 GLY n 1 84 VAL n 1 85 GLN n 1 86 ALA n 1 87 GLU n 1 88 ASP n 1 89 LEU n 1 90 ALA n 1 91 VAL n 1 92 TYR n 1 93 TYR n 1 94 CYS n 1 95 LYS n 1 96 GLN n 1 97 SER n 1 98 TYR n 1 99 ASN n 1 100 LEU n 1 101 ARG n 1 102 THR n 1 103 PHE n 1 104 GLY n 1 105 GLY n 1 106 GLY n 1 107 THR n 1 108 LYS n 1 109 LEU n 1 110 GLU n 1 111 LEU n 1 112 LYS n 2 1 GLU n 2 2 VAL n 2 3 LYS n 2 4 LEU n 2 5 VAL n 2 6 GLU n 2 7 SER n 2 8 GLY n 2 9 GLY n 2 10 GLY n 2 11 LEU n 2 12 VAL n 2 13 GLN n 2 14 PRO n 2 15 GLY n 2 16 GLY n 2 17 SER n 2 18 LEU n 2 19 ARG n 2 20 LEU n 2 21 SER n 2 22 CYS n 2 23 ALA n 2 24 THR n 2 25 SER n 2 26 GLY n 2 27 PHE n 2 28 THR n 2 29 PHE n 2 30 THR n 2 31 ASP n 2 32 TYR n 2 33 TYR n 2 34 MET n 2 35 SER n 2 36 TRP n 2 37 VAL n 2 38 ARG n 2 39 GLN n 2 40 PRO n 2 41 PRO n 2 42 GLY n 2 43 LYS n 2 44 ALA n 2 45 LEU n 2 46 GLU n 2 47 TRP n 2 48 LEU n 2 49 GLY n 2 50 PHE n 2 51 ILE n 2 52 ARG n 2 53 ASN n 2 54 LYS n 2 55 ALA n 2 56 LYS n 2 57 GLY n 2 58 TYR n 2 59 THR n 2 60 VAL n 2 61 GLU n 2 62 TYR n 2 63 SER n 2 64 ALA n 2 65 SER n 2 66 VAL n 2 67 LYS n 2 68 GLY n 2 69 ARG n 2 70 PHE n 2 71 THR n 2 72 ILE n 2 73 SER n 2 74 ARG n 2 75 ASP n 2 76 ASN n 2 77 SER n 2 78 GLN n 2 79 SER n 2 80 ILE n 2 81 LEU n 2 82 TYR n 2 83 LEU n 2 84 GLN n 2 85 MET n 2 86 ASN n 2 87 THR n 2 88 LEU n 2 89 ARG n 2 90 ALA n 2 91 GLU n 2 92 ASP n 2 93 SER n 2 94 ALA n 2 95 THR n 2 96 TYR n 2 97 TYR n 2 98 CYS n 2 99 ALA n 2 100 ARG n 2 101 ASP n 2 102 GLY n 2 103 TYR n 2 104 TYR n 2 105 VAL n 2 106 ASP n 2 107 ALA n 2 108 MET n 2 109 ASP n 2 110 TYR n 2 111 TRP n 2 112 GLY n 2 113 GLN n 2 114 GLY n 2 115 THR n 2 116 SER n 2 117 VAL n 2 118 THR n 2 119 VAL n 2 120 SER n 2 121 SER n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _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 _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _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 _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _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 _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 _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? mouse ? ? ? ? ? ? ? ? 'Mus Musculus' 10090 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? TG1 ? ? ? ? ? ? ? plasmid ? ? ? pSFJ8 ? ? 2 1 sample ? ? ? mouse ? ? ? ? ? ? ? ? 'Mus Musculus' 10090 ? ? ? ? ? ? ? ? 'Escherichia coli' 562 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.pdbx_db_accession _struct_ref.entity_id _struct_ref.pdbx_align_begin _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_db_isoform 1 PDB 3DV6 3DV6 1 ? ? ? 2 PDB 3DV6 3DV6 2 ? ? ? # 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 3DV6 A 1 ? 112 ? 3DV6 1 ? 106 ? 1 106 2 2 3DV6 B 1 ? 121 ? 3DV6 1 ? 113 ? 1 113 # 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 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 KDO 'D-saccharide, alpha linking' . '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' ? 'C8 H14 O8' 238.192 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 MG non-polymer . 'MAGNESIUM ION' ? 'Mg 2' 24.305 PG4 non-polymer . 'TETRAETHYLENE GLYCOL' ? 'C8 H18 O5' 194.226 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 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 3DV6 _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.10 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 41.51 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION' _exptl_crystal_grow.pH 8.5 _exptl_crystal_grow.temp 298 _exptl_crystal_grow.pdbx_details 'PEG 4000, MgCl2, pH 8.5, vapor diffusion, 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 'IMAGE PLATE' _diffrn_detector.type 'RIGAKU RAXIS IV++' _diffrn_detector.pdbx_collection_date ? _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 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU MICROMAX-002' _diffrn_source.pdbx_wavelength_list 1.5418 _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id 3DV6 _reflns.d_resolution_high 1.790 _reflns.d_resolution_low 20.000 _reflns.number_obs 21349 _reflns.pdbx_scaling_rejects 1432 _reflns.pdbx_Rmerge_I_obs 0.072 _reflns.pdbx_netI_over_sigmaI 15.700 _reflns.pdbx_chi_squared 1.000 _reflns.pdbx_redundancy 8.880 _reflns.percent_possible_obs 99.700 _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_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 1.79 1.86 ? 16906 ? 0.373 5.7 ? 1.180 8.36 ? 2014 96.70 ? 1 1.86 1.93 ? 18501 ? 0.358 5.8 ? 1.120 8.74 ? 2106 100.00 ? 2 1.93 2.02 ? 18517 ? 0.309 6.6 ? 1.080 8.80 ? 2092 100.00 ? 3 2.02 2.13 ? 18933 ? 0.264 7.5 ? 1.070 8.94 ? 2103 100.00 ? 4 2.13 2.26 ? 19435 ? 0.217 8.7 ? 1.030 9.09 ? 2123 100.00 ? 5 2.26 2.44 ? 19529 ? 0.177 10.4 ? 0.970 9.10 ? 2128 100.00 ? 6 2.44 2.68 ? 19471 ? 0.134 13.2 ? 0.930 9.11 ? 2125 100.00 ? 7 2.68 3.07 ? 19821 ? 0.089 18.7 ? 0.880 9.09 ? 2164 100.00 ? 8 3.07 3.86 ? 19939 ? 0.053 31.0 ? 0.880 9.02 ? 2185 100.00 ? 9 3.86 20.00 ? 19874 ? 0.035 46.5 ? 0.860 8.50 ? 2309 100.00 ? 10 # _refine.entry_id 3DV6 _refine.ls_d_res_high 1.950 _refine.ls_d_res_low 19.948 _refine.pdbx_ls_sigma_F 1.42 _refine.ls_percent_reflns_obs 99.980 _refine.ls_number_reflns_obs 16602 _refine.ls_R_factor_obs 0.233 _refine.ls_R_factor_R_work 0.229 _refine.ls_R_factor_R_free 0.303 _refine.ls_percent_reflns_R_free 4.990 _refine.ls_number_reflns_R_free 829 _refine.B_iso_mean 29.119 _refine.solvent_model_param_bsol 47.991 _refine.solvent_model_param_ksol 0.377 _refine.aniso_B[1][1] 0.163 _refine.aniso_B[2][2] 0.163 _refine.aniso_B[3][3] -0.326 _refine.aniso_B[1][2] 0.000 _refine.aniso_B[1][3] 0.000 _refine.aniso_B[2][3] 0.000 _refine.overall_SU_ML 0.360 _refine.solvent_model_details 'FLAT BULK SOLVENT MODEL' _refine.pdbx_solvent_vdw_probe_radii 1.110 _refine.pdbx_solvent_shrinkage_radii 0.900 _refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT' _refine.pdbx_stereochemistry_target_values ML _refine.B_iso_max 66.22 _refine.B_iso_min 15.07 _refine.occupancy_max 1.00 _refine.occupancy_min 1.00 _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_ls_cross_valid_method ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_isotropic_thermal_model ? _refine.details ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.pdbx_solvent_ion_probe_radii ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_B ? _refine.pdbx_overall_ESU_R_Free ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.pdbx_overall_ESU_R ? _refine.ls_wR_factor_R_free ? _refine.ls_wR_factor_R_work ? _refine.overall_FOM_free_R_set ? _refine.overall_FOM_work_R_set ? _refine.pdbx_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 1813 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 31 _refine_hist.number_atoms_solvent 131 _refine_hist.number_atoms_total 1975 _refine_hist.d_res_high 1.950 _refine_hist.d_res_low 19.948 # 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 1882 0.005 ? ? 'X-RAY DIFFRACTION' ? f_angle_d 2540 1.029 ? ? 'X-RAY DIFFRACTION' ? f_chiral_restr 274 0.068 ? ? 'X-RAY DIFFRACTION' ? f_plane_restr 319 0.003 ? ? 'X-RAY DIFFRACTION' ? f_dihedral_angle_d 670 19.903 ? ? '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 1.950 2.072 6 100.000 2561 . 0.264 0.332 . 135 . 2696 . . 'X-RAY DIFFRACTION' 2.072 2.232 6 100.000 2570 . 0.240 0.326 . 146 . 2716 . . 'X-RAY DIFFRACTION' 2.232 2.456 6 100.000 2582 . 0.249 0.327 . 146 . 2728 . . 'X-RAY DIFFRACTION' 2.456 2.811 6 100.000 2607 . 0.242 0.333 . 137 . 2744 . . 'X-RAY DIFFRACTION' 2.811 3.538 6 100.000 2643 . 0.225 0.326 . 142 . 2785 . . 'X-RAY DIFFRACTION' 3.538 19.949 6 100.000 2810 . 0.206 0.248 . 123 . 2933 . . 'X-RAY DIFFRACTION' # _struct.entry_id 3DV6 _struct.title 'Crystal structure of SAG506-01, tetragonal, crystal 2' _struct.pdbx_descriptor 'antibody Fv fragment SAG506-01, Ig-like protein' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3DV6 _struct_keywords.text 'antibody, KDO, twinning, pseudo-symmetry, IMMUNE SYSTEM' _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 ? D N N 3 ? E N N 4 ? F N N 5 ? G N N 6 ? H N N 6 ? # _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 GLN A 85 ? LEU A 89 ? GLN A 79 LEU A 83 5 ? 5 HELX_P HELX_P2 2 THR B 28 ? TYR B 32 ? THR B 28 TYR B 32 5 ? 5 HELX_P HELX_P3 3 ASN B 53 A GLY B 57 ? ASN B 52 GLY B 54 5 ? 5 HELX_P HELX_P4 4 ARG B 89 ? SER B 93 ? ARG B 83 SER B 87 5 ? 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role disulf1 disulf ? ? A CYS 23 SG ? ? ? 1_555 A CYS 94 SG ? ? A CYS 23 A CYS 88 1_555 ? ? ? ? ? ? ? 2.044 ? ? disulf2 disulf ? ? B CYS 22 SG ? ? ? 1_555 B CYS 98 SG ? ? B CYS 22 B CYS 92 1_555 ? ? ? ? ? ? ? 2.023 ? ? metalc1 metalc ? ? C MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 109 A HOH 121 1_555 ? ? ? ? ? ? ? 2.112 ? ? metalc2 metalc ? ? D MG . MG ? ? ? 1_555 G HOH . O ? ? A MG 110 A HOH 175 1_555 ? ? ? ? ? ? ? 2.400 ? ? # loop_ _struct_conn_type.id _struct_conn_type.criteria _struct_conn_type.reference disulf ? ? metalc ? ? # _struct_mon_prot_cis.pdbx_id 1 _struct_mon_prot_cis.label_comp_id SER _struct_mon_prot_cis.label_seq_id 7 _struct_mon_prot_cis.label_asym_id A _struct_mon_prot_cis.label_alt_id . _struct_mon_prot_cis.pdbx_PDB_ins_code ? _struct_mon_prot_cis.auth_comp_id SER _struct_mon_prot_cis.auth_seq_id 7 _struct_mon_prot_cis.auth_asym_id A _struct_mon_prot_cis.pdbx_label_comp_id_2 PRO _struct_mon_prot_cis.pdbx_label_seq_id_2 8 _struct_mon_prot_cis.pdbx_label_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_ins_code_2 ? _struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO _struct_mon_prot_cis.pdbx_auth_seq_id_2 8 _struct_mon_prot_cis.pdbx_auth_asym_id_2 A _struct_mon_prot_cis.pdbx_PDB_model_num 1 _struct_mon_prot_cis.pdbx_omega_angle -1.49 # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 4 ? B ? 6 ? C ? 4 ? D ? 2 ? E ? 4 ? F ? 6 ? G ? 4 ? # 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 B 1 2 ? parallel B 2 3 ? anti-parallel B 3 4 ? anti-parallel B 4 5 ? anti-parallel B 5 6 ? anti-parallel C 1 2 ? parallel C 2 3 ? anti-parallel C 3 4 ? anti-parallel D 1 2 ? anti-parallel E 1 2 ? anti-parallel E 2 3 ? anti-parallel E 3 4 ? anti-parallel F 1 2 ? parallel F 2 3 ? anti-parallel F 3 4 ? anti-parallel F 4 5 ? anti-parallel F 5 6 ? anti-parallel G 1 2 ? parallel G 2 3 ? anti-parallel G 3 4 ? 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 4 ? SER A 7 ? LEU A 4 SER A 7 A 2 ARG A 18 ? SER A 25 ? ARG A 18 SER A 25 A 3 ASP A 76 ? ASN A 82 ? ASP A 70 ASN A 76 A 4 PHE A 68 ? SER A 73 ? PHE A 62 SER A 67 B 1 SER A 10 ? VAL A 13 ? SER A 10 VAL A 13 B 2 THR A 107 ? LEU A 111 ? THR A 101 LEU A 105 B 3 ALA A 90 ? GLN A 96 ? ALA A 84 GLN A 90 B 4 LEU A 39 ? GLN A 44 ? LEU A 33 GLN A 38 B 5 LYS A 51 ? TYR A 55 ? LYS A 45 TYR A 49 B 6 THR A 59 ? ARG A 60 ? THR A 53 ARG A 54 C 1 SER A 10 ? VAL A 13 ? SER A 10 VAL A 13 C 2 THR A 107 ? LEU A 111 ? THR A 101 LEU A 105 C 3 ALA A 90 ? GLN A 96 ? ALA A 84 GLN A 90 C 4 THR A 102 ? PHE A 103 ? THR A 96 PHE A 97 D 1 PHE A 30 C LYS A 31 D PHE A 27 LYS A 27 D 2 LYS A 36 ? ASN A 37 ? LYS A 30 ASN A 31 E 1 LYS B 3 ? SER B 7 ? LYS B 3 SER B 7 E 2 LEU B 18 ? SER B 25 ? LEU B 18 SER B 25 E 3 ILE B 80 ? MET B 85 ? ILE B 77 MET B 82 E 4 PHE B 70 ? ASP B 75 ? PHE B 67 ASP B 72 F 1 GLY B 10 ? VAL B 12 ? GLY B 10 VAL B 12 F 2 THR B 115 ? VAL B 119 ? THR B 107 VAL B 111 F 3 ALA B 94 ? ASP B 101 ? ALA B 88 ASP B 95 F 4 TYR B 33 ? GLN B 39 ? TYR B 33 GLN B 39 F 5 GLU B 46 ? ILE B 51 ? GLU B 46 ILE B 51 F 6 VAL B 60 ? TYR B 62 ? VAL B 57 TYR B 59 G 1 GLY B 10 ? VAL B 12 ? GLY B 10 VAL B 12 G 2 THR B 115 ? VAL B 119 ? THR B 107 VAL B 111 G 3 ALA B 94 ? ASP B 101 ? ALA B 88 ASP B 95 G 4 TYR B 110 ? TRP B 111 ? TYR B 102 TRP B 103 # 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 N SER A 7 ? N SER A 7 O SER A 22 ? O SER A 22 A 2 3 N CYS A 23 ? N CYS A 23 O PHE A 77 ? O PHE A 71 A 3 4 O THR A 78 ? O THR A 72 N SER A 71 ? N SER A 65 B 1 2 N LEU A 11 ? N LEU A 11 O GLU A 110 ? O GLU A 104 B 2 3 O LEU A 109 ? O LEU A 103 N ALA A 90 ? N ALA A 84 B 3 4 O TYR A 93 ? O TYR A 87 N TYR A 42 ? N TYR A 36 B 4 5 N GLN A 43 ? N GLN A 37 O LYS A 51 ? O LYS A 45 B 5 6 N TYR A 55 ? N TYR A 49 O THR A 59 ? O THR A 53 C 1 2 N LEU A 11 ? N LEU A 11 O GLU A 110 ? O GLU A 104 C 2 3 O LEU A 109 ? O LEU A 103 N ALA A 90 ? N ALA A 84 C 3 4 N GLN A 96 ? N GLN A 90 O THR A 102 ? O THR A 96 D 1 2 N LYS A 31 D N LYS A 27 O LYS A 36 ? O LYS A 30 E 1 2 N SER B 7 ? N SER B 7 O SER B 21 ? O SER B 21 E 2 3 N LEU B 20 ? N LEU B 20 O LEU B 83 ? O LEU B 80 E 3 4 O ILE B 80 ? O ILE B 77 N ASP B 75 ? N ASP B 72 F 1 2 N GLY B 10 ? N GLY B 10 O THR B 118 ? O THR B 110 F 2 3 O VAL B 117 ? O VAL B 109 N ALA B 94 ? N ALA B 88 F 3 4 O TYR B 97 ? O TYR B 91 N VAL B 37 ? N VAL B 37 F 4 5 N ARG B 38 ? N ARG B 38 O GLU B 46 ? O GLU B 46 F 5 6 N PHE B 50 ? N PHE B 50 O GLU B 61 ? O GLU B 58 G 1 2 N GLY B 10 ? N GLY B 10 O THR B 118 ? O THR B 110 G 2 3 O VAL B 117 ? O VAL B 109 N ALA B 94 ? N ALA B 88 G 3 4 N ARG B 100 ? N ARG B 94 O TYR B 110 ? O TYR B 102 # _atom_sites.entry_id 3DV6 _atom_sites.fract_transf_matrix[1][1] 0.014002 _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] 0.014002 _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] 0.011754 _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 MG N O S # loop_ _database_PDB_caveat.text 'KDO B 114 HAS WRONG CHIRALITY AT ATOM C4' # 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 ASP 1 1 1 ASP ASP A . n A 1 2 ILE 2 2 2 ILE ILE A . n A 1 3 VAL 3 3 3 VAL VAL A . n A 1 4 LEU 4 4 4 LEU LEU A . n A 1 5 THR 5 5 5 THR THR A . n A 1 6 GLN 6 6 6 GLN GLN A . n A 1 7 SER 7 7 7 SER SER A . n A 1 8 PRO 8 8 8 PRO PRO A . n A 1 9 SER 9 9 9 SER SER A . n A 1 10 SER 10 10 10 SER SER A . n A 1 11 LEU 11 11 11 LEU LEU A . n A 1 12 ALA 12 12 12 ALA ALA A . n A 1 13 VAL 13 13 13 VAL VAL A . n A 1 14 SER 14 14 14 SER SER A . n A 1 15 ALA 15 15 15 ALA ALA A . n A 1 16 GLY 16 16 16 GLY GLY A . n A 1 17 GLU 17 17 17 GLU GLU A . n A 1 18 ARG 18 18 18 ARG ARG A . n A 1 19 VAL 19 19 19 VAL VAL A . n A 1 20 THR 20 20 20 THR THR A . n A 1 21 MET 21 21 21 MET MET A . n A 1 22 SER 22 22 22 SER SER A . n A 1 23 CYS 23 23 23 CYS CYS A . n A 1 24 LYS 24 24 24 LYS LYS A . n A 1 25 SER 25 25 25 SER SER A . n A 1 26 SER 26 26 26 SER SER A . n A 1 27 GLN 27 27 27 GLN GLN A . n A 1 28 SER 28 27 27 SER SER A A n A 1 29 LEU 29 27 27 LEU LEU A B n A 1 30 PHE 30 27 27 PHE PHE A C n A 1 31 LYS 31 27 27 LYS LYS A D n A 1 32 SER 32 27 27 SER SER A E n A 1 33 ARG 33 27 27 ARG ARG A F n A 1 34 ASN 34 28 28 ASN ASN A . n A 1 35 GLN 35 29 29 GLN GLN A . n A 1 36 LYS 36 30 30 LYS LYS A . n A 1 37 ASN 37 31 31 ASN ASN A . n A 1 38 TYR 38 32 32 TYR TYR A . n A 1 39 LEU 39 33 33 LEU LEU A . n A 1 40 ALA 40 34 34 ALA ALA A . n A 1 41 TRP 41 35 35 TRP TRP A . n A 1 42 TYR 42 36 36 TYR TYR A . n A 1 43 GLN 43 37 37 GLN GLN A . n A 1 44 GLN 44 38 38 GLN GLN A . n A 1 45 LYS 45 39 39 LYS LYS A . n A 1 46 PRO 46 40 40 PRO PRO A . n A 1 47 GLY 47 41 41 GLY GLY A . n A 1 48 GLN 48 42 42 GLN GLN A . n A 1 49 SER 49 43 43 SER SER A . n A 1 50 PRO 50 44 44 PRO PRO A . n A 1 51 LYS 51 45 45 LYS LYS A . n A 1 52 LEU 52 46 46 LEU LEU A . n A 1 53 LEU 53 47 47 LEU LEU A . n A 1 54 ILE 54 48 48 ILE ILE A . n A 1 55 TYR 55 49 49 TYR TYR A . n A 1 56 TRP 56 50 50 TRP TRP A . n A 1 57 ALA 57 51 51 ALA ALA A . n A 1 58 SER 58 52 52 SER SER A . n A 1 59 THR 59 53 53 THR THR A . n A 1 60 ARG 60 54 54 ARG ARG A . n A 1 61 GLU 61 55 55 GLU GLU A . n A 1 62 SER 62 56 56 SER SER A . n A 1 63 GLY 63 57 57 GLY GLY A . n A 1 64 VAL 64 58 58 VAL VAL A . n A 1 65 PRO 65 59 59 PRO PRO A . n A 1 66 ASP 66 60 60 ASP ASP A . n A 1 67 ARG 67 61 61 ARG ARG A . n A 1 68 PHE 68 62 62 PHE PHE A . n A 1 69 THR 69 63 63 THR THR A . n A 1 70 GLY 70 64 64 GLY GLY A . n A 1 71 SER 71 65 65 SER SER A . n A 1 72 GLY 72 66 66 GLY GLY A . n A 1 73 SER 73 67 67 SER SER A . n A 1 74 GLY 74 68 68 GLY GLY A . n A 1 75 THR 75 69 69 THR THR A . n A 1 76 ASP 76 70 70 ASP ASP A . n A 1 77 PHE 77 71 71 PHE PHE A . n A 1 78 THR 78 72 72 THR THR A . n A 1 79 LEU 79 73 73 LEU LEU A . n A 1 80 THR 80 74 74 THR THR A . n A 1 81 ILE 81 75 75 ILE ILE A . n A 1 82 ASN 82 76 76 ASN ASN A . n A 1 83 GLY 83 77 77 GLY GLY A . n A 1 84 VAL 84 78 78 VAL VAL A . n A 1 85 GLN 85 79 79 GLN GLN A . n A 1 86 ALA 86 80 80 ALA ALA A . n A 1 87 GLU 87 81 81 GLU GLU A . n A 1 88 ASP 88 82 82 ASP ASP A . n A 1 89 LEU 89 83 83 LEU LEU A . n A 1 90 ALA 90 84 84 ALA ALA A . n A 1 91 VAL 91 85 85 VAL VAL A . n A 1 92 TYR 92 86 86 TYR TYR A . n A 1 93 TYR 93 87 87 TYR TYR A . n A 1 94 CYS 94 88 88 CYS CYS A . n A 1 95 LYS 95 89 89 LYS LYS A . n A 1 96 GLN 96 90 90 GLN GLN A . n A 1 97 SER 97 91 91 SER SER A . n A 1 98 TYR 98 92 92 TYR TYR A . n A 1 99 ASN 99 93 93 ASN ASN A . n A 1 100 LEU 100 94 94 LEU LEU A . n A 1 101 ARG 101 95 95 ARG ARG A . n A 1 102 THR 102 96 96 THR THR A . n A 1 103 PHE 103 97 97 PHE PHE A . n A 1 104 GLY 104 98 98 GLY GLY A . n A 1 105 GLY 105 99 99 GLY GLY A . n A 1 106 GLY 106 100 100 GLY GLY A . n A 1 107 THR 107 101 101 THR THR A . n A 1 108 LYS 108 102 102 LYS LYS A . n A 1 109 LEU 109 103 103 LEU LEU A . n A 1 110 GLU 110 104 104 GLU GLU A . n A 1 111 LEU 111 105 105 LEU LEU A . n A 1 112 LYS 112 106 106 LYS LYS A . n B 2 1 GLU 1 1 1 GLU GLU B . n B 2 2 VAL 2 2 2 VAL VAL B . n B 2 3 LYS 3 3 3 LYS LYS B . n B 2 4 LEU 4 4 4 LEU LEU B . n B 2 5 VAL 5 5 5 VAL VAL B . n B 2 6 GLU 6 6 6 GLU GLU B . n B 2 7 SER 7 7 7 SER SER B . n B 2 8 GLY 8 8 8 GLY GLY B . n B 2 9 GLY 9 9 9 GLY GLY B . n B 2 10 GLY 10 10 10 GLY GLY B . n B 2 11 LEU 11 11 11 LEU LEU B . n B 2 12 VAL 12 12 12 VAL VAL B . n B 2 13 GLN 13 13 13 GLN GLN B . n B 2 14 PRO 14 14 14 PRO PRO B . n B 2 15 GLY 15 15 15 GLY GLY B . n B 2 16 GLY 16 16 16 GLY GLY B . n B 2 17 SER 17 17 17 SER SER B . n B 2 18 LEU 18 18 18 LEU LEU B . n B 2 19 ARG 19 19 19 ARG ARG B . n B 2 20 LEU 20 20 20 LEU LEU B . n B 2 21 SER 21 21 21 SER SER B . n B 2 22 CYS 22 22 22 CYS CYS B . n B 2 23 ALA 23 23 23 ALA ALA B . n B 2 24 THR 24 24 24 THR THR B . n B 2 25 SER 25 25 25 SER SER B . n B 2 26 GLY 26 26 26 GLY GLY B . n B 2 27 PHE 27 27 27 PHE PHE B . n B 2 28 THR 28 28 28 THR THR B . n B 2 29 PHE 29 29 29 PHE PHE B . n B 2 30 THR 30 30 30 THR THR B . n B 2 31 ASP 31 31 31 ASP ASP B . n B 2 32 TYR 32 32 32 TYR TYR B . n B 2 33 TYR 33 33 33 TYR TYR B . n B 2 34 MET 34 34 34 MET MET B . n B 2 35 SER 35 35 35 SER SER B . n B 2 36 TRP 36 36 36 TRP TRP B . n B 2 37 VAL 37 37 37 VAL VAL B . n B 2 38 ARG 38 38 38 ARG ARG B . n B 2 39 GLN 39 39 39 GLN GLN B . n B 2 40 PRO 40 40 40 PRO PRO B . n B 2 41 PRO 41 41 41 PRO PRO B . n B 2 42 GLY 42 42 42 GLY GLY B . n B 2 43 LYS 43 43 43 LYS LYS B . n B 2 44 ALA 44 44 44 ALA ALA B . n B 2 45 LEU 45 45 45 LEU LEU B . n B 2 46 GLU 46 46 46 GLU GLU B . n B 2 47 TRP 47 47 47 TRP TRP B . n B 2 48 LEU 48 48 48 LEU LEU B . n B 2 49 GLY 49 49 49 GLY GLY B . n B 2 50 PHE 50 50 50 PHE PHE B . n B 2 51 ILE 51 51 51 ILE ILE B . n B 2 52 ARG 52 52 52 ARG ARG B . n B 2 53 ASN 53 52 52 ASN ASN B A n B 2 54 LYS 54 52 52 LYS LYS B B n B 2 55 ALA 55 52 52 ALA ALA B C n B 2 56 LYS 56 53 53 LYS LYS B . n B 2 57 GLY 57 54 54 GLY GLY B . n B 2 58 TYR 58 55 55 TYR TYR B . n B 2 59 THR 59 56 56 THR THR B . n B 2 60 VAL 60 57 57 VAL VAL B . n B 2 61 GLU 61 58 58 GLU GLU B . n B 2 62 TYR 62 59 59 TYR TYR B . n B 2 63 SER 63 60 60 SER SER B . n B 2 64 ALA 64 61 61 ALA ALA B . n B 2 65 SER 65 62 62 SER SER B . n B 2 66 VAL 66 63 63 VAL VAL B . n B 2 67 LYS 67 64 64 LYS LYS B . n B 2 68 GLY 68 65 65 GLY GLY B . n B 2 69 ARG 69 66 66 ARG ARG B . n B 2 70 PHE 70 67 67 PHE PHE B . n B 2 71 THR 71 68 68 THR THR B . n B 2 72 ILE 72 69 69 ILE ILE B . n B 2 73 SER 73 70 70 SER SER B . n B 2 74 ARG 74 71 71 ARG ARG B . n B 2 75 ASP 75 72 72 ASP ASP B . n B 2 76 ASN 76 73 73 ASN ASN B . n B 2 77 SER 77 74 74 SER SER B . n B 2 78 GLN 78 75 75 GLN GLN B . n B 2 79 SER 79 76 76 SER SER B . n B 2 80 ILE 80 77 77 ILE ILE B . n B 2 81 LEU 81 78 78 LEU LEU B . n B 2 82 TYR 82 79 79 TYR TYR B . n B 2 83 LEU 83 80 80 LEU LEU B . n B 2 84 GLN 84 81 81 GLN GLN B . n B 2 85 MET 85 82 82 MET MET B . n B 2 86 ASN 86 82 82 ASN ASN B A n B 2 87 THR 87 82 82 THR THR B B n B 2 88 LEU 88 82 82 LEU LEU B C n B 2 89 ARG 89 83 83 ARG ARG B . n B 2 90 ALA 90 84 84 ALA ALA B . n B 2 91 GLU 91 85 85 GLU GLU B . n B 2 92 ASP 92 86 86 ASP ASP B . n B 2 93 SER 93 87 87 SER SER B . n B 2 94 ALA 94 88 88 ALA ALA B . n B 2 95 THR 95 89 89 THR THR B . n B 2 96 TYR 96 90 90 TYR TYR B . n B 2 97 TYR 97 91 91 TYR TYR B . n B 2 98 CYS 98 92 92 CYS CYS B . n B 2 99 ALA 99 93 93 ALA ALA B . n B 2 100 ARG 100 94 94 ARG ARG B . n B 2 101 ASP 101 95 95 ASP ASP B . n B 2 102 GLY 102 96 96 GLY GLY B . n B 2 103 TYR 103 97 97 TYR TYR B . n B 2 104 TYR 104 98 98 TYR TYR B . n B 2 105 VAL 105 99 99 VAL VAL B . n B 2 106 ASP 106 100 100 ASP ASP B . n B 2 107 ALA 107 100 100 ALA ALA B A n B 2 108 MET 108 100 100 MET MET B B n B 2 109 ASP 109 101 101 ASP ASP B . n B 2 110 TYR 110 102 102 TYR TYR B . n B 2 111 TRP 111 103 103 TRP TRP B . n B 2 112 GLY 112 104 104 GLY GLY B . n B 2 113 GLN 113 105 105 GLN GLN B . n B 2 114 GLY 114 106 106 GLY GLY B . n B 2 115 THR 115 107 107 THR THR B . n B 2 116 SER 116 108 108 SER SER B . n B 2 117 VAL 117 109 109 VAL VAL B . n B 2 118 THR 118 110 110 THR THR B . n B 2 119 VAL 119 111 111 VAL VAL B . n B 2 120 SER 120 112 112 SER SER B . n B 2 121 SER 121 113 113 SER SER 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 3 MG 1 109 109 MG MG A . D 3 MG 1 110 110 MG MG A . E 4 KDO 1 114 107 KDO KDO B . F 5 PG4 1 115 108 PG4 PG4 B . G 6 HOH 1 111 1 HOH HOH A . G 6 HOH 2 112 2 HOH HOH A . G 6 HOH 3 113 5 HOH HOH A . G 6 HOH 4 114 6 HOH HOH A . G 6 HOH 5 115 7 HOH HOH A . G 6 HOH 6 116 9 HOH HOH A . G 6 HOH 7 117 10 HOH HOH A . G 6 HOH 8 118 11 HOH HOH A . G 6 HOH 9 119 13 HOH HOH A . G 6 HOH 10 120 15 HOH HOH A . G 6 HOH 11 121 16 HOH HOH A . G 6 HOH 12 122 18 HOH HOH A . G 6 HOH 13 123 21 HOH HOH A . G 6 HOH 14 124 24 HOH HOH A . G 6 HOH 15 125 29 HOH HOH A . G 6 HOH 16 126 30 HOH HOH A . G 6 HOH 17 127 31 HOH HOH A . G 6 HOH 18 128 32 HOH HOH A . G 6 HOH 19 129 33 HOH HOH A . G 6 HOH 20 130 34 HOH HOH A . G 6 HOH 21 131 35 HOH HOH A . G 6 HOH 22 132 36 HOH HOH A . G 6 HOH 23 133 37 HOH HOH A . G 6 HOH 24 134 39 HOH HOH A . G 6 HOH 25 135 40 HOH HOH A . G 6 HOH 26 136 41 HOH HOH A . G 6 HOH 27 137 44 HOH HOH A . G 6 HOH 28 138 45 HOH HOH A . G 6 HOH 29 139 50 HOH HOH A . G 6 HOH 30 140 51 HOH HOH A . G 6 HOH 31 141 52 HOH HOH A . G 6 HOH 32 142 55 HOH HOH A . G 6 HOH 33 143 56 HOH HOH A . G 6 HOH 34 144 58 HOH HOH A . G 6 HOH 35 145 59 HOH HOH A . G 6 HOH 36 146 62 HOH HOH A . G 6 HOH 37 147 65 HOH HOH A . G 6 HOH 38 148 68 HOH HOH A . G 6 HOH 39 149 69 HOH HOH A . G 6 HOH 40 150 70 HOH HOH A . G 6 HOH 41 151 71 HOH HOH A . G 6 HOH 42 152 73 HOH HOH A . G 6 HOH 43 153 77 HOH HOH A . G 6 HOH 44 154 78 HOH HOH A . G 6 HOH 45 155 79 HOH HOH A . G 6 HOH 46 156 82 HOH HOH A . G 6 HOH 47 157 85 HOH HOH A . G 6 HOH 48 158 90 HOH HOH A . G 6 HOH 49 159 91 HOH HOH A . G 6 HOH 50 160 93 HOH HOH A . G 6 HOH 51 161 94 HOH HOH A . G 6 HOH 52 162 95 HOH HOH A . G 6 HOH 53 163 98 HOH HOH A . G 6 HOH 54 164 101 HOH HOH A . G 6 HOH 55 165 103 HOH HOH A . G 6 HOH 56 166 104 HOH HOH A . G 6 HOH 57 167 105 HOH HOH A . G 6 HOH 58 168 107 HOH HOH A . G 6 HOH 59 169 109 HOH HOH A . G 6 HOH 60 170 110 HOH HOH A . G 6 HOH 61 171 111 HOH HOH A . G 6 HOH 62 172 112 HOH HOH A . G 6 HOH 63 173 113 HOH HOH A . G 6 HOH 64 174 116 HOH HOH A . G 6 HOH 65 175 118 HOH HOH A . G 6 HOH 66 176 119 HOH HOH A . G 6 HOH 67 177 120 HOH HOH A . G 6 HOH 68 178 121 HOH HOH A . G 6 HOH 69 179 127 HOH HOH A . G 6 HOH 70 180 128 HOH HOH A . G 6 HOH 71 181 130 HOH HOH A . G 6 HOH 72 182 131 HOH HOH A . H 6 HOH 1 116 3 HOH HOH B . H 6 HOH 2 117 4 HOH HOH B . H 6 HOH 3 118 8 HOH HOH B . H 6 HOH 4 119 12 HOH HOH B . H 6 HOH 5 120 14 HOH HOH B . H 6 HOH 6 121 17 HOH HOH B . H 6 HOH 7 122 19 HOH HOH B . H 6 HOH 8 123 20 HOH HOH B . H 6 HOH 9 124 22 HOH HOH B . H 6 HOH 10 125 23 HOH HOH B . H 6 HOH 11 126 25 HOH HOH B . H 6 HOH 12 127 26 HOH HOH B . H 6 HOH 13 128 27 HOH HOH B . H 6 HOH 14 129 28 HOH HOH B . H 6 HOH 15 130 38 HOH HOH B . H 6 HOH 16 131 42 HOH HOH B . H 6 HOH 17 132 43 HOH HOH B . H 6 HOH 18 133 46 HOH HOH B . H 6 HOH 19 134 47 HOH HOH B . H 6 HOH 20 135 48 HOH HOH B . H 6 HOH 21 136 49 HOH HOH B . H 6 HOH 22 137 53 HOH HOH B . H 6 HOH 23 138 54 HOH HOH B . H 6 HOH 24 139 57 HOH HOH B . H 6 HOH 25 140 60 HOH HOH B . H 6 HOH 26 141 61 HOH HOH B . H 6 HOH 27 142 63 HOH HOH B . H 6 HOH 28 143 64 HOH HOH B . H 6 HOH 29 144 66 HOH HOH B . H 6 HOH 30 145 67 HOH HOH B . H 6 HOH 31 146 72 HOH HOH B . H 6 HOH 32 147 74 HOH HOH B . H 6 HOH 33 148 75 HOH HOH B . H 6 HOH 34 149 76 HOH HOH B . H 6 HOH 35 150 80 HOH HOH B . H 6 HOH 36 151 81 HOH HOH B . H 6 HOH 37 152 83 HOH HOH B . H 6 HOH 38 153 84 HOH HOH B . H 6 HOH 39 154 86 HOH HOH B . H 6 HOH 40 155 87 HOH HOH B . H 6 HOH 41 156 88 HOH HOH B . H 6 HOH 42 157 89 HOH HOH B . H 6 HOH 43 158 92 HOH HOH B . H 6 HOH 44 159 96 HOH HOH B . H 6 HOH 45 160 97 HOH HOH B . H 6 HOH 46 161 99 HOH HOH B . H 6 HOH 47 162 100 HOH HOH B . H 6 HOH 48 163 102 HOH HOH B . H 6 HOH 49 164 106 HOH HOH B . H 6 HOH 50 165 108 HOH HOH B . H 6 HOH 51 166 114 HOH HOH B . H 6 HOH 52 167 115 HOH HOH B . H 6 HOH 53 168 117 HOH HOH B . H 6 HOH 54 169 122 HOH HOH B . H 6 HOH 55 170 123 HOH HOH B . H 6 HOH 56 171 124 HOH HOH B . H 6 HOH 57 172 125 HOH HOH B . H 6 HOH 58 173 126 HOH HOH B . H 6 HOH 59 174 129 HOH HOH B . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H # 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)' 2710 ? 1 MORE -12 ? 1 'SSA (A^2)' 10020 ? # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1.0000000000 _pdbx_struct_oper_list.matrix[1][2] 0.0000000000 _pdbx_struct_oper_list.matrix[1][3] 0.0000000000 _pdbx_struct_oper_list.vector[1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][1] 0.0000000000 _pdbx_struct_oper_list.matrix[2][2] 1.0000000000 _pdbx_struct_oper_list.matrix[2][3] 0.0000000000 _pdbx_struct_oper_list.vector[2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][1] 0.0000000000 _pdbx_struct_oper_list.matrix[3][2] 0.0000000000 _pdbx_struct_oper_list.matrix[3][3] 1.0000000000 _pdbx_struct_oper_list.vector[3] 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2008-12-02 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2020-07-29 # loop_ _pdbx_audit_revision_details.ordinal _pdbx_audit_revision_details.revision_ordinal _pdbx_audit_revision_details.data_content_type _pdbx_audit_revision_details.provider _pdbx_audit_revision_details.type _pdbx_audit_revision_details.description _pdbx_audit_revision_details.details 1 1 'Structure model' repository 'Initial release' ? ? 2 3 'Structure model' repository Remediation 'Carbohydrate remediation' ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' Advisory 3 3 'Structure model' 'Data collection' 4 3 'Structure model' 'Derived calculations' 5 3 'Structure model' 'Structure summary' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' chem_comp 2 3 'Structure model' database_PDB_caveat 3 3 'Structure model' entity 4 3 'Structure model' pdbx_chem_comp_identifier 5 3 'Structure model' pdbx_entity_nonpoly 6 3 'Structure model' struct_site 7 3 'Structure model' struct_site_gen # 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' '_chem_comp.name' 2 3 'Structure model' '_chem_comp.type' 3 3 'Structure model' '_entity.pdbx_description' 4 3 'Structure model' '_pdbx_entity_nonpoly.name' # _pdbx_phasing_MR.entry_id 3DV6 _pdbx_phasing_MR.method_rotation ? _pdbx_phasing_MR.method_translation ? _pdbx_phasing_MR.model_details 'Phaser MODE: MR_AUTO' _pdbx_phasing_MR.R_factor 39.710 _pdbx_phasing_MR.R_rigid_body ? _pdbx_phasing_MR.correlation_coeff_Fo_to_Fc ? _pdbx_phasing_MR.correlation_coeff_Io_to_Ic ? _pdbx_phasing_MR.d_res_high_rotation 2.500 _pdbx_phasing_MR.d_res_low_rotation 19.950 _pdbx_phasing_MR.d_res_high_translation 2.500 _pdbx_phasing_MR.d_res_low_translation 19.950 _pdbx_phasing_MR.packing ? _pdbx_phasing_MR.reflns_percent_rotation ? _pdbx_phasing_MR.reflns_percent_translation ? _pdbx_phasing_MR.sigma_F_rotation ? _pdbx_phasing_MR.sigma_F_translation ? _pdbx_phasing_MR.sigma_I_rotation ? _pdbx_phasing_MR.sigma_I_translation ? # _phasing.method MR # 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 d*TREK . ? package 'Jim W. Pflugrath' Jim.Pflugrath@Rigaku.com 'data scaling' http://www.rigaku.com/software/dtrek.html ? ? 1 PHASER . ? program 'Randy J. Read' cimr-phaser@lists.cam.ac.uk phasing http://www-structmed.cimr.cam.ac.uk/phaser/ ? ? 2 PHENIX . ? package 'Paul D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 3 PDB_EXTRACT 3.006 'June 11, 2008' package PDB help@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 4 d*TREK . ? ? ? ? 'data reduction' ? ? ? 5 # 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 ARG A 27 F ? -29.11 -57.78 2 1 ALA A 51 ? ? 73.84 -44.77 3 1 ALA A 84 ? ? 178.47 170.91 4 1 LEU A 94 ? ? 53.19 -137.12 # _pdbx_validate_chiral.id 1 _pdbx_validate_chiral.PDB_model_num 1 _pdbx_validate_chiral.auth_atom_id C4 _pdbx_validate_chiral.label_alt_id ? _pdbx_validate_chiral.auth_asym_id B _pdbx_validate_chiral.auth_comp_id KDO _pdbx_validate_chiral.auth_seq_id 114 _pdbx_validate_chiral.PDB_ins_code ? _pdbx_validate_chiral.details 'WRONG HAND' _pdbx_validate_chiral.omega . # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier KDO 'CONDENSED IUPAC CARBOHYDRATE SYMBOL' GMML 1.0 DKdopa KDO 'IUPAC CARBOHYDRATE SYMBOL' PDB-CARE 1.0 a-D-Kdop KDO 'SNFG CARBOHYDRATE SYMBOL' GMML 1.0 Kdo # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'MAGNESIUM ION' MG 4 '3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid' KDO 5 'TETRAETHYLENE GLYCOL' PG4 6 water HOH #