data_3E5D # _entry.id 3E5D # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.365 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code _database_2.pdbx_database_accession _database_2.pdbx_DOI PDB 3E5D pdb_00003e5d 10.2210/pdb3e5d/pdb RCSB RCSB048895 ? ? WWPDB D_1000048895 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 367570 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 3E5D _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2008-08-13 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.methods_development_category ? _pdbx_database_status.status_code_nmr_data ? # _audit_author.name 'Joint Center for Structural Genomics (JCSG)' _audit_author.pdbx_ordinal 1 # _citation.id primary _citation.title 'Crystal structure of Putative Glyoxalase I (YP_013033.1) from LISTERIA MONOCYTOGENES 4b F2365 at 2.70 A resolution' _citation.journal_abbrev 'To be published' _citation.journal_volume ? _citation.page_first ? _citation.page_last ? _citation.year ? _citation.journal_id_ASTM ? _citation.country ? _citation.journal_id_ISSN ? _citation.journal_id_CSD 0353 _citation.book_publisher ? _citation.pdbx_database_id_PubMed ? _citation.pdbx_database_id_DOI ? # _citation_author.citation_id primary _citation_author.name 'Joint Center for Structural Genomics (JCSG)' _citation_author.ordinal 1 _citation_author.identifier_ORCID ? # _cell.entry_id 3E5D _cell.length_a 123.590 _cell.length_b 123.590 _cell.length_c 123.590 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.pdbx_unique_axis ? _cell.Z_PDB 24 _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 3E5D _symmetry.Int_Tables_number 199 _symmetry.space_group_name_H-M 'I 21 3' _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 'Putative Glyoxalase I' 14502.468 1 ? ? ? ? 2 non-polymer syn 'UNKNOWN LIGAND' ? 1 ? ? ? ? 3 water nat water 18.015 2 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer yes _entity_poly.pdbx_seq_one_letter_code ;G(MSE)KIEHVALWTTNLEQ(MSE)KQFYVTYFGATANDLYENKTKGFNSYFLSFEDGARLEI(MSE)SRTDVTGKTTGE NLGWAHIAISTGTKEAVDELTEKLRQDGFAIAGEPR(MSE)TGDGYYESVVLDPEGNRIEITW ; _entity_poly.pdbx_seq_one_letter_code_can ;GMKIEHVALWTTNLEQMKQFYVTYFGATANDLYENKTKGFNSYFLSFEDGARLEIMSRTDVTGKTTGENLGWAHIAISTG TKEAVDELTEKLRQDGFAIAGEPRMTGDGYYESVVLDPEGNRIEITW ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 367570 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 MSE n 1 3 LYS n 1 4 ILE n 1 5 GLU n 1 6 HIS n 1 7 VAL n 1 8 ALA n 1 9 LEU n 1 10 TRP n 1 11 THR n 1 12 THR n 1 13 ASN n 1 14 LEU n 1 15 GLU n 1 16 GLN n 1 17 MSE n 1 18 LYS n 1 19 GLN n 1 20 PHE n 1 21 TYR n 1 22 VAL n 1 23 THR n 1 24 TYR n 1 25 PHE n 1 26 GLY n 1 27 ALA n 1 28 THR n 1 29 ALA n 1 30 ASN n 1 31 ASP n 1 32 LEU n 1 33 TYR n 1 34 GLU n 1 35 ASN n 1 36 LYS n 1 37 THR n 1 38 LYS n 1 39 GLY n 1 40 PHE n 1 41 ASN n 1 42 SER n 1 43 TYR n 1 44 PHE n 1 45 LEU n 1 46 SER n 1 47 PHE n 1 48 GLU n 1 49 ASP n 1 50 GLY n 1 51 ALA n 1 52 ARG n 1 53 LEU n 1 54 GLU n 1 55 ILE n 1 56 MSE n 1 57 SER n 1 58 ARG n 1 59 THR n 1 60 ASP n 1 61 VAL n 1 62 THR n 1 63 GLY n 1 64 LYS n 1 65 THR n 1 66 THR n 1 67 GLY n 1 68 GLU n 1 69 ASN n 1 70 LEU n 1 71 GLY n 1 72 TRP n 1 73 ALA n 1 74 HIS n 1 75 ILE n 1 76 ALA n 1 77 ILE n 1 78 SER n 1 79 THR n 1 80 GLY n 1 81 THR n 1 82 LYS n 1 83 GLU n 1 84 ALA n 1 85 VAL n 1 86 ASP n 1 87 GLU n 1 88 LEU n 1 89 THR n 1 90 GLU n 1 91 LYS n 1 92 LEU n 1 93 ARG n 1 94 GLN n 1 95 ASP n 1 96 GLY n 1 97 PHE n 1 98 ALA n 1 99 ILE n 1 100 ALA n 1 101 GLY n 1 102 GLU n 1 103 PRO n 1 104 ARG n 1 105 MSE n 1 106 THR n 1 107 GLY n 1 108 ASP n 1 109 GLY n 1 110 TYR n 1 111 TYR n 1 112 GLU n 1 113 SER n 1 114 VAL n 1 115 VAL n 1 116 LEU n 1 117 ASP n 1 118 PRO n 1 119 GLU n 1 120 GLY n 1 121 ASN n 1 122 ARG n 1 123 ILE n 1 124 GLU n 1 125 ILE n 1 126 THR n 1 127 TRP 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 ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene LMOf2365_0426 _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 'Listeria monocytogenes str. 4b F2365' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 265669 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc ? _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia Coli' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562 _entity_src_gen.host_org_genus ? _entity_src_gen.pdbx_host_org_gene ? _entity_src_gen.pdbx_host_org_organ ? _entity_src_gen.host_org_species ? _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain HK100 _entity_src_gen.pdbx_host_org_variant ? _entity_src_gen.pdbx_host_org_cell_line ? _entity_src_gen.pdbx_host_org_atcc ? _entity_src_gen.pdbx_host_org_culture_collection ? _entity_src_gen.pdbx_host_org_cell ? _entity_src_gen.pdbx_host_org_organelle ? _entity_src_gen.pdbx_host_org_cellular_location ? _entity_src_gen.pdbx_host_org_vector_type Plasmid _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name SpeedET _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q723Q1_LISMF _struct_ref.pdbx_db_accession Q723Q1 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MKIEHVALWTTNLEQMKQFYVTYFGATANDLYENKTKGFNSYFLSFEDGARLEIMSRTDVTGKTTGENLGWAHIAISTGT KEAVDELTEKLRQDGFAIAGEPRMTGDGYYESVVLDPEGNRIEITW ; _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3E5D _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 Q723Q1 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 126 _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 126 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 3E5D _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 Q723Q1 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 0 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MSE 'L-peptide linking' n SELENOMETHIONINE ? 'C5 H11 N O2 Se' 196.106 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 UNL non-polymer . 'UNKNOWN LIGAND' ? ? ? VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.method 'X-RAY DIFFRACTION' _exptl.entry_id 3E5D # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 5.42 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 77.32 _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 277 _exptl_crystal_grow.pdbx_details ;1.1M sodium citrate, 0.15M sodium chloride, 0.1M TRIS pH 7.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, 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 'MARMOSAIC 325 mm CCD' _diffrn_detector.details 'Flat mirror (vertical focusing)' _diffrn_detector.pdbx_collection_date 2008-05-27 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Single crystal Si(111) bent monochromator (horizontal focusing)' _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength . _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline BL11-1 _diffrn_source.type 'SSRL BEAMLINE BL11-1' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list ? _diffrn_source.pdbx_synchrotron_site SSRL # _reflns.entry_id 3E5D _reflns.d_resolution_high 2.70 _reflns.d_resolution_low 29.136 _reflns.number_obs 8775 _reflns.pdbx_Rmerge_I_obs 0.051 _reflns.percent_possible_obs 99.700 _reflns.B_iso_Wilson_estimate 103.91 _reflns.observed_criterion_sigma_I -3.00 _reflns.observed_criterion_sigma_F ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 22.200 _reflns.pdbx_redundancy ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_chi_squared ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_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 2.70 2.80 13982 ? 1700 0.991 2.2 ? ? ? ? ? 98.80 1 1 2.80 2.91 14401 ? 1656 0.605 3.6 ? ? ? ? ? 100.00 2 1 2.91 3.04 14216 ? 1633 0.351 6.1 ? ? ? ? ? 100.00 3 1 3.04 3.20 14719 ? 1690 0.192 10.5 ? ? ? ? ? 100.00 4 1 3.20 3.40 14587 ? 1677 0.106 17.6 ? ? ? ? ? 100.00 5 1 3.40 3.66 14329 ? 1652 0.075 23.2 ? ? ? ? ? 99.90 6 1 3.66 4.03 14500 ? 1683 0.051 33.0 ? ? ? ? ? 100.00 7 1 4.03 4.60 14395 ? 1669 0.040 39.4 ? ? ? ? ? 99.90 8 1 4.60 5.77 14186 ? 1644 0.036 42.0 ? ? ? ? ? 100.00 9 1 5.77 29.136 14583 ? 1722 0.034 44.1 ? ? ? ? ? 98.70 10 1 # _refine.entry_id 3E5D _refine.ls_d_res_high 2.700 _refine.ls_d_res_low 29.136 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 99.800 _refine.ls_number_reflns_obs 8766 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details ;1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. AN UNKNOWN LIGAND (UNL) HAS BEEN TENTATIVELY MODELED AT WHAT APPEARS TO BE THE PUTATIVE ACTIVE SITE(S) SURROUNDED BY RESIDUES HIS5, PHE39, GLU53, ARG57, HIS73, ASP107, GLU111 AND GLU123. ; _refine.ls_R_factor_obs 0.173 _refine.ls_R_factor_R_work 0.172 _refine.ls_R_factor_R_free 0.198 _refine.ls_percent_reflns_R_free 4.700 _refine.ls_number_reflns_R_free 416 _refine.B_iso_mean 57.474 _refine.correlation_coeff_Fo_to_Fc 0.970 _refine.correlation_coeff_Fo_to_Fc_free 0.964 _refine.pdbx_overall_ESU_R 0.228 _refine.pdbx_overall_ESU_R_Free 0.189 _refine.overall_SU_ML 0.127 _refine.overall_SU_B 13.998 _refine.solvent_model_details MASK _refine.pdbx_solvent_vdw_probe_radii 1.200 _refine.pdbx_solvent_ion_probe_radii 0.800 _refine.pdbx_solvent_shrinkage_radii 0.800 _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD WITH PHASES' _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.aniso_B[1][1] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][2] ? _refine.aniso_B[2][3] ? _refine.aniso_B[3][3] ? _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.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_TLS_residual_ADP_flag 'LIKELY RESIDUAL' _refine.pdbx_diffrn_id 1 _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 996 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 9 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 1007 _refine_hist.d_res_high 2.700 _refine_hist.d_res_low 29.136 # 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 1017 0.012 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 666 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1378 1.657 1.935 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1618 0.959 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 125 4.031 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 50 29.224 24.600 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 168 12.377 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 5 19.148 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 150 0.095 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1150 0.005 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 216 0.001 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 179 0.218 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 647 0.185 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 494 0.188 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 520 0.085 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 32 0.376 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 5 0.147 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 27 0.206 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 3 0.216 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 681 1.373 3.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 261 0.243 3.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 995 2.134 5.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 449 3.973 8.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 383 5.127 11.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 2.701 _refine_ls_shell.d_res_low 2.771 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 100.000 _refine_ls_shell.number_reflns_R_work 607 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.427 _refine_ls_shell.R_factor_R_free 0.504 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 35 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 642 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 3E5D _struct.title 'Crystal structure of a putative glyoxalase i (lmof2365_0426) from listeria monocytogenes str. 4b f2365 at 2.70 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text 'Structural genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, lyase' _struct_keywords.pdbx_keywords LYASE _struct_keywords.entry_id 3E5D # 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 ;AUTHORS STATE THAT THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS THAT FORM A DIMER BASED ON CRYSTAL PACKING ANALYSIS. ; # 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 ASN A 13 ? GLY A 26 ? ASN A 12 GLY A 25 1 ? 14 HELX_P HELX_P2 2 THR A 81 ? ASP A 95 ? THR A 80 ASP A 94 1 ? 15 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order _struct_conn.pdbx_role covale1 covale both ? A MSE 2 C ? ? ? 1_555 A LYS 3 N ? ? A MSE 1 A LYS 2 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale2 covale both ? A GLN 16 C ? ? ? 1_555 A MSE 17 N ? ? A GLN 15 A MSE 16 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale3 covale both ? A MSE 17 C ? ? ? 1_555 A LYS 18 N ? ? A MSE 16 A LYS 17 1_555 ? ? ? ? ? ? ? 1.326 ? ? covale4 covale both ? A ILE 55 C ? ? ? 1_555 A MSE 56 N ? ? A ILE 54 A MSE 55 1_555 ? ? ? ? ? ? ? 1.325 ? ? covale5 covale both ? A MSE 56 C ? ? ? 1_555 A SER 57 N ? ? A MSE 55 A SER 56 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale6 covale both ? A ARG 104 C ? ? ? 1_555 A MSE 105 N ? ? A ARG 103 A MSE 104 1_555 ? ? ? ? ? ? ? 1.330 ? ? covale7 covale both ? A MSE 105 C ? ? ? 1_555 A THR 106 N ? ? A MSE 104 A THR 105 1_555 ? ? ? ? ? ? ? 1.326 ? ? # _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 ? 4 ? B ? 4 ? C ? 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 ? 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 C 1 2 ? parallel C 2 3 ? anti-parallel C 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 HIS A 6 ? TRP A 10 ? HIS A 5 TRP A 9 A 2 ARG A 52 ? ARG A 58 ? ARG A 51 ARG A 57 A 3 PHE A 40 ? SER A 46 ? PHE A 39 SER A 45 A 4 THR A 28 ? ALA A 29 ? THR A 27 ALA A 28 B 1 HIS A 6 ? TRP A 10 ? HIS A 5 TRP A 9 B 2 ARG A 52 ? ARG A 58 ? ARG A 51 ARG A 57 B 3 PHE A 40 ? SER A 46 ? PHE A 39 SER A 45 B 4 TYR A 33 ? ASN A 35 ? TYR A 32 ASN A 34 C 1 ILE A 75 ? SER A 78 ? ILE A 74 SER A 77 C 2 ARG A 122 ? THR A 126 ? ARG A 121 THR A 125 C 3 TYR A 111 ? LEU A 116 ? TYR A 110 LEU A 115 C 4 ILE A 99 ? MSE A 105 ? ILE A 98 MSE A 104 # 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 LEU A 9 ? N LEU A 8 O GLU A 54 ? O GLU A 53 A 2 3 O LEU A 53 ? O LEU A 52 N LEU A 45 ? N LEU A 44 A 3 4 O SER A 46 ? O SER A 45 N THR A 28 ? N THR A 27 B 1 2 N LEU A 9 ? N LEU A 8 O GLU A 54 ? O GLU A 53 B 2 3 O LEU A 53 ? O LEU A 52 N LEU A 45 ? N LEU A 44 B 3 4 O SER A 42 ? O SER A 41 N TYR A 33 ? N TYR A 32 C 1 2 N ILE A 75 ? N ILE A 74 O GLU A 124 ? O GLU A 123 C 2 3 O ILE A 125 ? O ILE A 124 N SER A 113 ? N SER A 112 C 3 4 O VAL A 114 ? O VAL A 113 N GLY A 101 ? N GLY A 100 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id UNL _struct_site.pdbx_auth_seq_id 200 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 9 _struct_site.details 'BINDING SITE FOR RESIDUE UNL A 200' # 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 9 HIS A 6 ? HIS A 5 . ? 14_655 ? 2 AC1 9 ASN A 35 ? ASN A 34 . ? 14_655 ? 3 AC1 9 PHE A 40 ? PHE A 39 . ? 14_655 ? 4 AC1 9 GLU A 54 ? GLU A 53 . ? 14_655 ? 5 AC1 9 ARG A 58 ? ARG A 57 . ? 14_655 ? 6 AC1 9 THR A 106 ? THR A 105 . ? 1_555 ? 7 AC1 9 ASP A 108 ? ASP A 107 . ? 1_555 ? 8 AC1 9 GLU A 112 ? GLU A 111 . ? 1_555 ? 9 AC1 9 GLU A 124 ? GLU A 123 . ? 1_555 ? # _atom_sites.entry_id 3E5D _atom_sites.fract_transf_matrix[1][1] 0.008091 _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] 0.008091 _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] 0.008091 _atom_sites.fract_transf_vector[1] 0.000000 _atom_sites.fract_transf_vector[2] 0.000000 _atom_sites.fract_transf_vector[3] 0.000000 # loop_ _atom_type.symbol C N O SE # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id _pdbx_poly_seq_scheme.pdb_ins_code _pdbx_poly_seq_scheme.hetero A 1 1 GLY 1 0 ? ? ? A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 LYS 3 2 2 LYS LYS A . n A 1 4 ILE 4 3 3 ILE ILE A . n A 1 5 GLU 5 4 4 GLU GLU A . n A 1 6 HIS 6 5 5 HIS HIS A . n A 1 7 VAL 7 6 6 VAL VAL A . n A 1 8 ALA 8 7 7 ALA ALA A . n A 1 9 LEU 9 8 8 LEU LEU A . n A 1 10 TRP 10 9 9 TRP TRP A . n A 1 11 THR 11 10 10 THR THR A . n A 1 12 THR 12 11 11 THR THR A . n A 1 13 ASN 13 12 12 ASN ASN A . n A 1 14 LEU 14 13 13 LEU LEU A . n A 1 15 GLU 15 14 14 GLU GLU A . n A 1 16 GLN 16 15 15 GLN GLN A . n A 1 17 MSE 17 16 16 MSE MSE A . n A 1 18 LYS 18 17 17 LYS LYS A . n A 1 19 GLN 19 18 18 GLN GLN A . n A 1 20 PHE 20 19 19 PHE PHE A . n A 1 21 TYR 21 20 20 TYR TYR A . n A 1 22 VAL 22 21 21 VAL VAL A . n A 1 23 THR 23 22 22 THR THR A . n A 1 24 TYR 24 23 23 TYR TYR A . n A 1 25 PHE 25 24 24 PHE PHE A . n A 1 26 GLY 26 25 25 GLY GLY A . n A 1 27 ALA 27 26 26 ALA ALA A . n A 1 28 THR 28 27 27 THR THR A . n A 1 29 ALA 29 28 28 ALA ALA A . n A 1 30 ASN 30 29 29 ASN ASN A . n A 1 31 ASP 31 30 30 ASP ASP A . n A 1 32 LEU 32 31 31 LEU LEU A . n A 1 33 TYR 33 32 32 TYR TYR A . n A 1 34 GLU 34 33 33 GLU GLU A . n A 1 35 ASN 35 34 34 ASN ASN A . n A 1 36 LYS 36 35 35 LYS LYS A . n A 1 37 THR 37 36 36 THR THR A . n A 1 38 LYS 38 37 37 LYS LYS A . n A 1 39 GLY 39 38 38 GLY GLY A . n A 1 40 PHE 40 39 39 PHE PHE A . n A 1 41 ASN 41 40 40 ASN ASN A . n A 1 42 SER 42 41 41 SER SER A . n A 1 43 TYR 43 42 42 TYR TYR A . n A 1 44 PHE 44 43 43 PHE PHE A . n A 1 45 LEU 45 44 44 LEU LEU A . n A 1 46 SER 46 45 45 SER SER A . n A 1 47 PHE 47 46 46 PHE PHE A . n A 1 48 GLU 48 47 47 GLU GLU A . n A 1 49 ASP 49 48 48 ASP ASP A . n A 1 50 GLY 50 49 49 GLY GLY A . n A 1 51 ALA 51 50 50 ALA ALA A . n A 1 52 ARG 52 51 51 ARG ARG A . n A 1 53 LEU 53 52 52 LEU LEU A . n A 1 54 GLU 54 53 53 GLU GLU A . n A 1 55 ILE 55 54 54 ILE ILE A . n A 1 56 MSE 56 55 55 MSE MSE A . n A 1 57 SER 57 56 56 SER SER A . n A 1 58 ARG 58 57 57 ARG ARG A . n A 1 59 THR 59 58 58 THR THR A . n A 1 60 ASP 60 59 59 ASP ASP A . n A 1 61 VAL 61 60 60 VAL VAL A . n A 1 62 THR 62 61 61 THR THR A . n A 1 63 GLY 63 62 62 GLY GLY A . n A 1 64 LYS 64 63 63 LYS LYS A . n A 1 65 THR 65 64 64 THR THR A . n A 1 66 THR 66 65 65 THR THR A . n A 1 67 GLY 67 66 66 GLY GLY A . n A 1 68 GLU 68 67 67 GLU GLU A . n A 1 69 ASN 69 68 68 ASN ASN A . n A 1 70 LEU 70 69 69 LEU LEU A . n A 1 71 GLY 71 70 70 GLY GLY A . n A 1 72 TRP 72 71 71 TRP TRP A . n A 1 73 ALA 73 72 72 ALA ALA A . n A 1 74 HIS 74 73 73 HIS HIS A . n A 1 75 ILE 75 74 74 ILE ILE A . n A 1 76 ALA 76 75 75 ALA ALA A . n A 1 77 ILE 77 76 76 ILE ILE A . n A 1 78 SER 78 77 77 SER SER A . n A 1 79 THR 79 78 78 THR THR A . n A 1 80 GLY 80 79 79 GLY GLY A . n A 1 81 THR 81 80 80 THR THR A . n A 1 82 LYS 82 81 81 LYS LYS A . n A 1 83 GLU 83 82 82 GLU GLU A . n A 1 84 ALA 84 83 83 ALA ALA A . n A 1 85 VAL 85 84 84 VAL VAL A . n A 1 86 ASP 86 85 85 ASP ASP A . n A 1 87 GLU 87 86 86 GLU GLU A . n A 1 88 LEU 88 87 87 LEU LEU A . n A 1 89 THR 89 88 88 THR THR A . n A 1 90 GLU 90 89 89 GLU GLU A . n A 1 91 LYS 91 90 90 LYS LYS A . n A 1 92 LEU 92 91 91 LEU LEU A . n A 1 93 ARG 93 92 92 ARG ARG A . n A 1 94 GLN 94 93 93 GLN GLN A . n A 1 95 ASP 95 94 94 ASP ASP A . n A 1 96 GLY 96 95 95 GLY GLY A . n A 1 97 PHE 97 96 96 PHE PHE A . n A 1 98 ALA 98 97 97 ALA ALA A . n A 1 99 ILE 99 98 98 ILE ILE A . n A 1 100 ALA 100 99 99 ALA ALA A . n A 1 101 GLY 101 100 100 GLY GLY A . n A 1 102 GLU 102 101 101 GLU GLU A . n A 1 103 PRO 103 102 102 PRO PRO A . n A 1 104 ARG 104 103 103 ARG ARG A . n A 1 105 MSE 105 104 104 MSE MSE A . n A 1 106 THR 106 105 105 THR THR A . n A 1 107 GLY 107 106 106 GLY GLY A . n A 1 108 ASP 108 107 107 ASP ASP A . n A 1 109 GLY 109 108 108 GLY GLY A . n A 1 110 TYR 110 109 109 TYR TYR A . n A 1 111 TYR 111 110 110 TYR TYR A . n A 1 112 GLU 112 111 111 GLU GLU A . n A 1 113 SER 113 112 112 SER SER A . n A 1 114 VAL 114 113 113 VAL VAL A . n A 1 115 VAL 115 114 114 VAL VAL A . n A 1 116 LEU 116 115 115 LEU LEU A . n A 1 117 ASP 117 116 116 ASP ASP A . n A 1 118 PRO 118 117 117 PRO PRO A . n A 1 119 GLU 119 118 118 GLU GLU A . n A 1 120 GLY 120 119 119 GLY GLY A . n A 1 121 ASN 121 120 120 ASN ASN A . n A 1 122 ARG 122 121 121 ARG ARG A . n A 1 123 ILE 123 122 122 ILE ILE A . n A 1 124 GLU 124 123 123 GLU GLU A . n A 1 125 ILE 125 124 124 ILE ILE A . n A 1 126 THR 126 125 125 THR THR A . n A 1 127 TRP 127 126 126 TRP TRP A . n # _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Joint Center for Structural Genomics' _pdbx_SG_project.id 1 _pdbx_SG_project.initial_of_center JCSG # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 UNL 1 200 200 UNL UNL A . C 3 HOH 1 201 1 HOH HOH A . C 3 HOH 2 202 2 HOH HOH A . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 2 A MSE 1 ? MET SELENOMETHIONINE 2 A MSE 17 A MSE 16 ? MET SELENOMETHIONINE 3 A MSE 56 A MSE 55 ? MET SELENOMETHIONINE 4 A MSE 105 A MSE 104 ? MET SELENOMETHIONINE # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 _pdbx_struct_assembly_gen.asym_id_list A,B,C # 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)' 4980 ? 1 MORE -35 ? 1 'SSA (A^2)' 11530 ? # 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' 14_655 -x+1,-y+1/2,z -1.0000000000 0.0000000000 0.0000000000 123.5900000000 0.0000000000 -1.0000000000 0.0000000000 61.7950000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_audit_revision_history.ordinal _pdbx_audit_revision_history.data_content_type _pdbx_audit_revision_history.major_revision _pdbx_audit_revision_history.minor_revision _pdbx_audit_revision_history.revision_date 1 'Structure model' 1 0 2008-08-26 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2017-10-25 4 'Structure model' 1 3 2019-07-24 5 'Structure model' 1 4 2023-02-01 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? _pdbx_audit_revision_details.details ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' Advisory 2 2 'Structure model' 'Version format compliance' 3 3 'Structure model' 'Refinement description' 4 4 'Structure model' 'Data collection' 5 4 'Structure model' 'Derived calculations' 6 4 'Structure model' 'Refinement description' 7 5 'Structure model' 'Database references' 8 5 'Structure model' 'Derived calculations' # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 3 'Structure model' software 2 4 'Structure model' software 3 4 'Structure model' struct_conn 4 5 'Structure model' database_2 5 5 'Structure model' struct_ref_seq_dif 6 5 'Structure model' struct_site # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 3 'Structure model' '_software.classification' 2 3 'Structure model' '_software.name' 3 4 'Structure model' '_software.classification' 4 4 'Structure model' '_software.contact_author' 5 4 'Structure model' '_software.contact_author_email' 6 4 'Structure model' '_software.language' 7 4 'Structure model' '_software.location' 8 4 'Structure model' '_software.name' 9 4 'Structure model' '_software.type' 10 4 'Structure model' '_software.version' 11 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 12 5 'Structure model' '_database_2.pdbx_DOI' 13 5 'Structure model' '_database_2.pdbx_database_accession' 14 5 'Structure model' '_struct_ref_seq_dif.details' 15 5 'Structure model' '_struct_site.pdbx_auth_asym_id' 16 5 'Structure model' '_struct_site.pdbx_auth_comp_id' 17 5 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 59.8985 _pdbx_refine_tls.origin_y 22.1081 _pdbx_refine_tls.origin_z 31.8695 _pdbx_refine_tls.T[1][1] 0.0249 _pdbx_refine_tls.T[2][2] 0.0818 _pdbx_refine_tls.T[3][3] -0.0103 _pdbx_refine_tls.T[1][2] -0.0146 _pdbx_refine_tls.T[1][3] 0.0023 _pdbx_refine_tls.T[2][3] -0.0445 _pdbx_refine_tls.L[1][1] 3.7815 _pdbx_refine_tls.L[2][2] 3.0936 _pdbx_refine_tls.L[3][3] 1.2344 _pdbx_refine_tls.L[1][2] -1.3178 _pdbx_refine_tls.L[1][3] 0.6147 _pdbx_refine_tls.L[2][3] 0.1987 _pdbx_refine_tls.S[1][1] 0.1110 _pdbx_refine_tls.S[2][2] -0.0806 _pdbx_refine_tls.S[3][3] -0.0303 _pdbx_refine_tls.S[1][2] 0.4266 _pdbx_refine_tls.S[1][3] -0.3703 _pdbx_refine_tls.S[2][3] 0.2793 _pdbx_refine_tls.S[2][1] -0.2088 _pdbx_refine_tls.S[3][1] 0.1659 _pdbx_refine_tls.S[3][2] -0.0032 _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_label_asym_id A _pdbx_refine_tls_group.beg_label_seq_id 2 _pdbx_refine_tls_group.end_label_asym_id A _pdbx_refine_tls_group.end_label_seq_id 127 _pdbx_refine_tls_group.selection ? _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 1 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 126 _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 REFMAC 5.2.0019 ? program 'Murshudov, G.N.' ccp4@dl.ac.uk refinement http://www.ccp4.ac.uk/main.html Fortran_77 ? 1 PHENIX . ? package 'P.D. Adams' PDAdams@lbl.gov refinement http://www.phenix-online.org/ C++ ? 2 SHELX . ? package 'George Sheldrick' gsheldr@shelx.uni-ac.gwdg.de phasing http://shelx.uni-ac.gwdg.de/SHELX/ Fortran_77 ? 3 MolProbity 3beta29 ? package 'D.C. & J.S. Richardson lab' molprobity@kinemage.biochem.duke.edu 'model building' http://kinemage.biochem.duke.edu/molprobity/ ? ? 4 XSCALE . ? package 'Wolfgang Kabsch' ? 'data scaling' http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/xscale_program.html ? ? 5 PDB_EXTRACT 3.004 'September 10, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 XDS . ? ? ? ? 'data reduction' ? ? ? 7 SHELXD . ? ? ? ? phasing ? ? ? 8 autoSHARP . ? ? ? ? phasing ? ? ? 9 # _pdbx_entry_details.entry_id 3E5D _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. HOWEVER, ABOUT 5-10% OF THE PURIFIED PROTEIN HAS THE TAG ON BUT THIS IS NOT VISIBLE IN THE ELECTRON DENSITY OF THE STRUCTURE. IT IS NOT KNOWN IF CRYSTALLIZATION SELECTED FOR TAG OFF MOLECULES OR IF PARTIAL OCCUPANCY AND DISORDER MAKE THE TAG UNOBSERVABLE. ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id PHE _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 46 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi -106.51 _pdbx_validate_torsion.psi -156.70 # 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 35 ? CD ? A LYS 36 CD 2 1 Y 1 A LYS 35 ? CE ? A LYS 36 CE 3 1 Y 1 A LYS 35 ? NZ ? A LYS 36 NZ 4 1 Y 1 A LYS 63 ? CD ? A LYS 64 CD 5 1 Y 1 A LYS 63 ? CE ? A LYS 64 CE 6 1 Y 1 A LYS 63 ? NZ ? A LYS 64 NZ 7 1 Y 1 A GLU 86 ? OE1 ? A GLU 87 OE1 8 1 Y 1 A GLU 86 ? OE2 ? A GLU 87 OE2 # _pdbx_unobs_or_zero_occ_residues.id 1 _pdbx_unobs_or_zero_occ_residues.PDB_model_num 1 _pdbx_unobs_or_zero_occ_residues.polymer_flag Y _pdbx_unobs_or_zero_occ_residues.occupancy_flag 1 _pdbx_unobs_or_zero_occ_residues.auth_asym_id A _pdbx_unobs_or_zero_occ_residues.auth_comp_id GLY _pdbx_unobs_or_zero_occ_residues.auth_seq_id 0 _pdbx_unobs_or_zero_occ_residues.PDB_ins_code ? _pdbx_unobs_or_zero_occ_residues.label_asym_id A _pdbx_unobs_or_zero_occ_residues.label_comp_id GLY _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'UNKNOWN LIGAND' UNL 3 water HOH #