data_3GHD # _entry.id 3GHD # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.357 _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 3GHD pdb_00003ghd 10.2210/pdb3ghd/pdb RCSB RCSB051861 ? ? WWPDB D_1000051861 ? ? # _pdbx_database_PDB_obs_spr.id SPRSDE _pdbx_database_PDB_obs_spr.date 2009-03-31 _pdbx_database_PDB_obs_spr.pdb_id 3GHD _pdbx_database_PDB_obs_spr.replace_pdb_id 3FIO _pdbx_database_PDB_obs_spr.details ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id APC40009 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 3GHD _pdbx_database_status.recvd_initial_deposition_date 2009-03-03 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry Y _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data ? # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Dong, A.' 1 ? 'Xu, X.' 2 ? 'Chruszcz, M.' 3 ? 'Brown, G.' 4 ? 'Proudfoot, M.' 5 ? 'Edwards, A.M.' 6 ? 'Joachimiak, A.' 7 ? 'Minor, W.' 8 0000-0001-7075-7090 'Savchenko, A.' 9 ? 'Yaleunin, A.' 10 ? 'Midwest Center for Structural Genomics (MCSG)' 11 ? # _citation.id primary _citation.title 'Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain' _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 _citation_author.identifier_ORCID primary 'Dong, A.' 1 ? primary 'Xu, X.' 2 ? primary 'Chruszcz, M.' 3 ? primary 'Brown, G.' 4 ? primary 'Proudfoot, M.' 5 ? primary 'Edwards, A.M.' 6 ? primary 'Joachimiak, A.' 7 ? primary 'Minor, W.' 8 0000-0001-7075-7090 primary 'Savchenko, A.' 9 ? primary 'Yaleunin, A.' 10 ? # _cell.entry_id 3GHD _cell.length_a 54.153 _cell.length_b 73.162 _cell.length_c 35.264 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.entry_id 3GHD _symmetry.space_group_name_H-M 'P 21 21 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _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 'a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain' 7746.842 2 ? ? ? ? 2 water nat water 18.015 112 ? ? ? ? # _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 'KAIVVQPKDTVDRVAKILSRNKAGSAVV(MSE)EGDEILGVVTERDILDKVVAKGKNPKEVKVEEI(MSE)TKNPVKI' _entity_poly.pdbx_seq_one_letter_code_can KAIVVQPKDTVDRVAKILSRNKAGSAVVMEGDEILGVVTERDILDKVVAKGKNPKEVKVEEIMTKNPVKI _entity_poly.pdbx_strand_id A,B _entity_poly.pdbx_target_identifier APC40009 # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 LYS n 1 2 ALA n 1 3 ILE n 1 4 VAL n 1 5 VAL n 1 6 GLN n 1 7 PRO n 1 8 LYS n 1 9 ASP n 1 10 THR n 1 11 VAL n 1 12 ASP n 1 13 ARG n 1 14 VAL n 1 15 ALA n 1 16 LYS n 1 17 ILE n 1 18 LEU n 1 19 SER n 1 20 ARG n 1 21 ASN n 1 22 LYS n 1 23 ALA n 1 24 GLY n 1 25 SER n 1 26 ALA n 1 27 VAL n 1 28 VAL n 1 29 MSE n 1 30 GLU n 1 31 GLY n 1 32 ASP n 1 33 GLU n 1 34 ILE n 1 35 LEU n 1 36 GLY n 1 37 VAL n 1 38 VAL n 1 39 THR n 1 40 GLU n 1 41 ARG n 1 42 ASP n 1 43 ILE n 1 44 LEU n 1 45 ASP n 1 46 LYS n 1 47 VAL n 1 48 VAL n 1 49 ALA n 1 50 LYS n 1 51 GLY n 1 52 LYS n 1 53 ASN n 1 54 PRO n 1 55 LYS n 1 56 GLU n 1 57 VAL n 1 58 LYS n 1 59 VAL n 1 60 GLU n 1 61 GLU n 1 62 ILE n 1 63 MSE n 1 64 THR n 1 65 LYS n 1 66 ASN n 1 67 PRO n 1 68 VAL n 1 69 LYS n 1 70 ILE 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 ? _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 'Pyrococcus furiosus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2261 _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)DERIVATIVE' _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 'PET DERIVATIVE' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code Q8TZN4_PYRFU _struct_ref.pdbx_db_accession Q8TZN4 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code KAIVVQPKDTVDRVAKILSRNKAGSAVVMEGDEILGVVTERDILDKVVAKGKNPKEVKVEEIMTKNPVKI _struct_ref.pdbx_align_begin 14 _struct_ref.pdbx_db_isoform ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 3GHD A 1 ? 70 ? Q8TZN4 14 ? 83 ? 14 83 2 1 3GHD B 1 ? 70 ? Q8TZN4 14 ? 83 ? 14 83 # 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 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 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 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.entry_id 3GHD _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.25 _exptl_crystal.density_percent_sol 45.44 _exptl_crystal.description ? _exptl_crystal.F_000 ? _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 297 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details '0.2M Ammonium Chloride,20%PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K' _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 unsupported-m300 _diffrn_detector.pdbx_collection_date 2008-10-20 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 0.97941 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'APS BEAMLINE 23-ID-B' _diffrn_source.pdbx_synchrotron_site APS _diffrn_source.pdbx_synchrotron_beamline 23-ID-B _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.97941 # _reflns.entry_id 3GHD _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 50 _reflns.d_resolution_high 1.8 _reflns.number_obs 11994 _reflns.number_all 11994 _reflns.percent_possible_obs 89.5 _reflns.pdbx_Rmerge_I_obs 0.094 _reflns.pdbx_Rsym_value 0.094 _reflns.pdbx_netI_over_sigmaI 14.6 _reflns.B_iso_Wilson_estimate 18.4 _reflns.pdbx_redundancy 6.2 _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 # _reflns_shell.d_res_high 1.8 _reflns_shell.d_res_low 1.86 _reflns_shell.percent_possible_all 61.0 _reflns_shell.Rmerge_I_obs 0.202 _reflns_shell.pdbx_Rsym_value 0.202 _reflns_shell.meanI_over_sigI_obs 5.84 _reflns_shell.pdbx_redundancy 3.6 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 798 _reflns_shell.number_measured_all ? _reflns_shell.number_measured_obs ? _reflns_shell.number_unique_obs ? _reflns_shell.pdbx_chi_squared ? _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1 # _refine.entry_id 3GHD _refine.ls_number_reflns_obs 11368 _refine.ls_number_reflns_all 11368 _refine.pdbx_ls_sigma_I 0 _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 31.77 _refine.ls_d_res_high 1.81 _refine.ls_percent_reflns_obs 89.09 _refine.ls_R_factor_obs 0.19455 _refine.ls_R_factor_all 0.19455 _refine.ls_R_factor_R_work 0.19229 _refine.ls_R_factor_R_free 0.24108 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 596 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.956 _refine.correlation_coeff_Fo_to_Fc_free 0.921 _refine.B_iso_mean 13.171 _refine.aniso_B[1][1] -0.50 _refine.aniso_B[2][2] 1.49 _refine.aniso_B[3][3] -0.99 _refine.aniso_B[1][2] 0.00 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.40 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOMIC B-FACTORS ARE RESIDUALS FROM TLS REFINEMENT.' _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.150 _refine.pdbx_overall_ESU_R_Free 0.146 _refine.overall_SU_ML 0.093 _refine.overall_SU_B 6.635 _refine.ls_redundancy_reflns_obs ? _refine.B_iso_min ? _refine.B_iso_max ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _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 1027 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 112 _refine_hist.number_atoms_total 1139 _refine_hist.d_res_high 1.81 _refine_hist.d_res_low 31.77 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.019 0.022 ? 1031 'X-RAY DIFFRACTION' ? r_bond_other_d 0.001 0.020 ? 685 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.807 2.000 ? 1393 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.056 3.000 ? 1724 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.740 5.000 ? 138 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 38.852 28.125 ? 32 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 16.528 15.000 ? 206 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 15.451 15.000 ? 3 'X-RAY DIFFRACTION' ? r_chiral_restr 0.112 0.200 ? 182 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.007 0.021 ? 1103 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.001 0.020 ? 144 'X-RAY DIFFRACTION' ? r_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 0.853 1.500 ? 696 'X-RAY DIFFRACTION' ? r_mcbond_other 0.271 1.500 ? 280 'X-RAY DIFFRACTION' ? r_mcangle_it 1.375 2.000 ? 1137 'X-RAY DIFFRACTION' ? r_scbond_it 2.677 3.000 ? 335 'X-RAY DIFFRACTION' ? r_scangle_it 4.293 4.500 ? 256 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_restr_ncs.dom_id _refine_ls_restr_ncs.pdbx_auth_asym_id _refine_ls_restr_ncs.pdbx_number _refine_ls_restr_ncs.rms_dev_position _refine_ls_restr_ncs.weight_position _refine_ls_restr_ncs.pdbx_type _refine_ls_restr_ncs.pdbx_ens_id _refine_ls_restr_ncs.pdbx_ordinal _refine_ls_restr_ncs.pdbx_refine_id _refine_ls_restr_ncs.ncs_model_details _refine_ls_restr_ncs.rms_dev_B_iso _refine_ls_restr_ncs.weight_B_iso 1 A 755 0.34 0.50 'medium positional' 1 1 'X-RAY DIFFRACTION' ? ? ? 1 A 755 0.86 2.00 'medium thermal' 1 2 'X-RAY DIFFRACTION' ? ? ? # _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.805 _refine_ls_shell.d_res_low 1.852 _refine_ls_shell.number_reflns_R_work 535 _refine_ls_shell.R_factor_R_work 0.196 _refine_ls_shell.percent_reflns_obs 58.29 _refine_ls_shell.R_factor_R_free 0.243 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 31 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # loop_ _struct_ncs_dom.id _struct_ncs_dom.details _struct_ncs_dom.pdbx_ens_id 1 A 1 2 B 1 # _struct_ncs_ens.id 1 _struct_ncs_ens.details ? # _struct.entry_id 3GHD _struct.title 'Crystal structure of a cystathionine beta-synthase domain protein fused to a Zn-ribbon-like domain' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3GHD _struct_keywords.pdbx_keywords 'Nucleotide binding protein, Metal binding protein' _struct_keywords.text ;PF1953, APC40009, cystathionine beta-synthase domain protein, Structural Genomics, PSI-2, Protein Structure Initiative, Midwest Center for Structural Genomics, MCSG, NUCLEOTIDE BINDING PROTEIN, METAL BINDIN, Metal binding protein ; # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 1 ? C N N 2 ? D N N 2 ? # _struct_biol.id 1 _struct_biol.details ? # loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 1 THR A 10 ? ASN A 21 ? THR A 23 ASN A 34 1 ? 12 HELX_P HELX_P2 2 GLU A 40 ? VAL A 47 ? GLU A 53 VAL A 60 1 ? 8 HELX_P HELX_P3 3 ASN A 53 ? VAL A 57 ? ASN A 66 VAL A 70 5 ? 5 HELX_P HELX_P4 4 LYS A 58 ? ILE A 62 ? LYS A 71 ILE A 75 5 ? 5 HELX_P HELX_P5 5 THR B 10 ? ASN B 21 ? THR B 23 ASN B 34 1 ? 12 HELX_P HELX_P6 6 GLU B 40 ? VAL B 47 ? GLU B 53 VAL B 60 1 ? 8 HELX_P HELX_P7 7 ASN B 53 ? VAL B 57 ? ASN B 66 VAL B 70 5 ? 5 HELX_P HELX_P8 8 LYS B 58 ? ILE B 62 ? LYS B 71 ILE B 75 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 covale1 covale both ? A VAL 28 C ? ? ? 1_555 A MSE 29 N ? ? A VAL 41 A MSE 42 1_555 ? ? ? ? ? ? ? 1.337 ? ? covale2 covale both ? A MSE 29 C ? ? ? 1_555 A GLU 30 N ? ? A MSE 42 A GLU 43 1_555 ? ? ? ? ? ? ? 1.333 ? ? covale3 covale both ? A ILE 62 C ? ? ? 1_555 A MSE 63 N ? ? A ILE 75 A MSE 76 1_555 ? ? ? ? ? ? ? 1.332 ? ? covale4 covale both ? A MSE 63 C ? ? ? 1_555 A THR 64 N ? ? A MSE 76 A THR 77 1_555 ? ? ? ? ? ? ? 1.320 ? ? covale5 covale both ? B VAL 28 C ? ? ? 1_555 B MSE 29 N ? ? B VAL 41 B MSE 42 1_555 ? ? ? ? ? ? ? 1.334 ? ? covale6 covale both ? B MSE 29 C ? ? ? 1_555 B GLU 30 N ? ? B MSE 42 B GLU 43 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale7 covale both ? B ILE 62 C ? ? ? 1_555 B MSE 63 N ? ? B ILE 75 B MSE 76 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale8 covale both ? B MSE 63 C ? ? ? 1_555 B THR 64 N ? ? B MSE 76 B THR 77 1_555 ? ? ? ? ? ? ? 1.328 ? ? # _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 ? 3 ? # 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 # 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 ALA A 2 ? VAL A 5 ? ALA A 15 VAL A 18 A 2 SER A 25 ? GLU A 30 ? SER A 38 GLU A 43 A 3 GLU A 33 ? THR A 39 ? GLU A 46 THR A 52 A 4 THR A 64 ? LYS A 65 ? THR A 77 LYS A 78 B 1 ALA B 2 ? VAL B 5 ? ALA B 15 VAL B 18 B 2 SER B 25 ? GLU B 30 ? SER B 38 GLU B 43 B 3 GLU B 33 ? THR B 39 ? GLU B 46 THR B 52 # 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 VAL A 5 ? N VAL A 18 O MSE A 29 ? O MSE A 42 A 2 3 N ALA A 26 ? N ALA A 39 O VAL A 38 ? O VAL A 51 A 3 4 N VAL A 37 ? N VAL A 50 O THR A 64 ? O THR A 77 B 1 2 N VAL B 5 ? N VAL B 18 O MSE B 29 ? O MSE B 42 B 2 3 N GLU B 30 ? N GLU B 43 O GLU B 33 ? O GLU B 46 # _database_PDB_matrix.entry_id 3GHD _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id 3GHD _atom_sites.fract_transf_matrix[1][1] 0.018466 _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] 0.013668 _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] 0.028358 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O 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 LYS 1 14 14 LYS LYS A . n A 1 2 ALA 2 15 15 ALA ALA A . n A 1 3 ILE 3 16 16 ILE ILE A . n A 1 4 VAL 4 17 17 VAL VAL A . n A 1 5 VAL 5 18 18 VAL VAL A . n A 1 6 GLN 6 19 19 GLN GLN A . n A 1 7 PRO 7 20 20 PRO PRO A . n A 1 8 LYS 8 21 21 LYS LYS A . n A 1 9 ASP 9 22 22 ASP ASP A . n A 1 10 THR 10 23 23 THR THR A . n A 1 11 VAL 11 24 24 VAL VAL A . n A 1 12 ASP 12 25 25 ASP ASP A . n A 1 13 ARG 13 26 26 ARG ARG A . n A 1 14 VAL 14 27 27 VAL VAL A . n A 1 15 ALA 15 28 28 ALA ALA A . n A 1 16 LYS 16 29 29 LYS LYS A . n A 1 17 ILE 17 30 30 ILE ILE A . n A 1 18 LEU 18 31 31 LEU LEU A . n A 1 19 SER 19 32 32 SER SER A . n A 1 20 ARG 20 33 33 ARG ARG A . n A 1 21 ASN 21 34 34 ASN ASN A . n A 1 22 LYS 22 35 35 LYS LYS A . n A 1 23 ALA 23 36 36 ALA ALA A . n A 1 24 GLY 24 37 37 GLY GLY A . n A 1 25 SER 25 38 38 SER SER A . n A 1 26 ALA 26 39 39 ALA ALA A . n A 1 27 VAL 27 40 40 VAL VAL A . n A 1 28 VAL 28 41 41 VAL VAL A . n A 1 29 MSE 29 42 42 MSE MSE A . n A 1 30 GLU 30 43 43 GLU GLU A . n A 1 31 GLY 31 44 44 GLY GLY A . n A 1 32 ASP 32 45 45 ASP ASP A . n A 1 33 GLU 33 46 46 GLU GLU A . n A 1 34 ILE 34 47 47 ILE ILE A . n A 1 35 LEU 35 48 48 LEU LEU A . n A 1 36 GLY 36 49 49 GLY GLY A . n A 1 37 VAL 37 50 50 VAL VAL A . n A 1 38 VAL 38 51 51 VAL VAL A . n A 1 39 THR 39 52 52 THR THR A . n A 1 40 GLU 40 53 53 GLU GLU A . n A 1 41 ARG 41 54 54 ARG ARG A . n A 1 42 ASP 42 55 55 ASP ASP A . n A 1 43 ILE 43 56 56 ILE ILE A . n A 1 44 LEU 44 57 57 LEU LEU A . n A 1 45 ASP 45 58 58 ASP ASP A . n A 1 46 LYS 46 59 59 LYS LYS A . n A 1 47 VAL 47 60 60 VAL VAL A . n A 1 48 VAL 48 61 61 VAL VAL A . n A 1 49 ALA 49 62 62 ALA ALA A . n A 1 50 LYS 50 63 63 LYS LYS A . n A 1 51 GLY 51 64 64 GLY GLY A . n A 1 52 LYS 52 65 65 LYS LYS A . n A 1 53 ASN 53 66 66 ASN ASN A . n A 1 54 PRO 54 67 67 PRO PRO A . n A 1 55 LYS 55 68 68 LYS LYS A . n A 1 56 GLU 56 69 69 GLU GLU A . n A 1 57 VAL 57 70 70 VAL VAL A . n A 1 58 LYS 58 71 71 LYS LYS A . n A 1 59 VAL 59 72 72 VAL VAL A . n A 1 60 GLU 60 73 73 GLU GLU A . n A 1 61 GLU 61 74 74 GLU GLU A . n A 1 62 ILE 62 75 75 ILE ILE A . n A 1 63 MSE 63 76 76 MSE MSE A . n A 1 64 THR 64 77 77 THR THR A . n A 1 65 LYS 65 78 78 LYS LYS A . n A 1 66 ASN 66 79 79 ASN ASN A . n A 1 67 PRO 67 80 80 PRO PRO A . n A 1 68 VAL 68 81 81 VAL VAL A . n A 1 69 LYS 69 82 82 LYS LYS A . n A 1 70 ILE 70 83 83 ILE ILE A . n B 1 1 LYS 1 14 14 LYS LYS B . n B 1 2 ALA 2 15 15 ALA ALA B . n B 1 3 ILE 3 16 16 ILE ILE B . n B 1 4 VAL 4 17 17 VAL VAL B . n B 1 5 VAL 5 18 18 VAL VAL B . n B 1 6 GLN 6 19 19 GLN GLN B . n B 1 7 PRO 7 20 20 PRO PRO B . n B 1 8 LYS 8 21 21 LYS LYS B . n B 1 9 ASP 9 22 22 ASP ASP B . n B 1 10 THR 10 23 23 THR THR B . n B 1 11 VAL 11 24 24 VAL VAL B . n B 1 12 ASP 12 25 25 ASP ASP B . n B 1 13 ARG 13 26 26 ARG ARG B . n B 1 14 VAL 14 27 27 VAL VAL B . n B 1 15 ALA 15 28 28 ALA ALA B . n B 1 16 LYS 16 29 29 LYS LYS B . n B 1 17 ILE 17 30 30 ILE ILE B . n B 1 18 LEU 18 31 31 LEU LEU B . n B 1 19 SER 19 32 32 SER SER B . n B 1 20 ARG 20 33 33 ARG ARG B . n B 1 21 ASN 21 34 34 ASN ASN B . n B 1 22 LYS 22 35 35 LYS LYS B . n B 1 23 ALA 23 36 36 ALA ALA B . n B 1 24 GLY 24 37 37 GLY GLY B . n B 1 25 SER 25 38 38 SER SER B . n B 1 26 ALA 26 39 39 ALA ALA B . n B 1 27 VAL 27 40 40 VAL VAL B . n B 1 28 VAL 28 41 41 VAL VAL B . n B 1 29 MSE 29 42 42 MSE MSE B . n B 1 30 GLU 30 43 43 GLU GLU B . n B 1 31 GLY 31 44 44 GLY GLY B . n B 1 32 ASP 32 45 45 ASP ASP B . n B 1 33 GLU 33 46 46 GLU GLU B . n B 1 34 ILE 34 47 47 ILE ILE B . n B 1 35 LEU 35 48 48 LEU LEU B . n B 1 36 GLY 36 49 49 GLY GLY B . n B 1 37 VAL 37 50 50 VAL VAL B . n B 1 38 VAL 38 51 51 VAL VAL B . n B 1 39 THR 39 52 52 THR THR B . n B 1 40 GLU 40 53 53 GLU GLU B . n B 1 41 ARG 41 54 54 ARG ARG B . n B 1 42 ASP 42 55 55 ASP ASP B . n B 1 43 ILE 43 56 56 ILE ILE B . n B 1 44 LEU 44 57 57 LEU LEU B . n B 1 45 ASP 45 58 58 ASP ASP B . n B 1 46 LYS 46 59 59 LYS LYS B . n B 1 47 VAL 47 60 60 VAL VAL B . n B 1 48 VAL 48 61 61 VAL VAL B . n B 1 49 ALA 49 62 62 ALA ALA B . n B 1 50 LYS 50 63 63 LYS LYS B . n B 1 51 GLY 51 64 64 GLY GLY B . n B 1 52 LYS 52 65 65 LYS LYS B . n B 1 53 ASN 53 66 66 ASN ASN B . n B 1 54 PRO 54 67 67 PRO PRO B . n B 1 55 LYS 55 68 68 LYS LYS B . n B 1 56 GLU 56 69 69 GLU GLU B . n B 1 57 VAL 57 70 70 VAL VAL B . n B 1 58 LYS 58 71 71 LYS LYS B . n B 1 59 VAL 59 72 72 VAL VAL B . n B 1 60 GLU 60 73 73 GLU GLU B . n B 1 61 GLU 61 74 74 GLU GLU B . n B 1 62 ILE 62 75 75 ILE ILE B . n B 1 63 MSE 63 76 76 MSE MSE B . n B 1 64 THR 64 77 77 THR THR B . n B 1 65 LYS 65 78 78 LYS LYS B . n B 1 66 ASN 66 79 79 ASN ASN B . n B 1 67 PRO 67 80 80 PRO PRO B . n B 1 68 VAL 68 81 81 VAL VAL B . n B 1 69 LYS 69 82 82 LYS LYS B . n B 1 70 ILE 70 83 83 ILE ILE B . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name 'PSI, Protein Structure Initiative' _pdbx_SG_project.full_name_of_center 'Midwest Center for Structural Genomics' _pdbx_SG_project.initial_of_center MCSG # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code C 2 HOH 1 1 1 HOH HOH A . C 2 HOH 2 2 2 HOH HOH A . C 2 HOH 3 3 3 HOH HOH A . C 2 HOH 4 4 4 HOH HOH A . C 2 HOH 5 6 6 HOH HOH A . C 2 HOH 6 7 7 HOH HOH A . C 2 HOH 7 8 8 HOH HOH A . C 2 HOH 8 9 9 HOH HOH A . C 2 HOH 9 10 10 HOH HOH A . C 2 HOH 10 11 11 HOH HOH A . C 2 HOH 11 12 12 HOH HOH A . C 2 HOH 12 13 13 HOH HOH A . C 2 HOH 13 84 14 HOH HOH A . C 2 HOH 14 85 15 HOH HOH A . C 2 HOH 15 86 16 HOH HOH A . C 2 HOH 16 87 17 HOH HOH A . C 2 HOH 17 88 18 HOH HOH A . C 2 HOH 18 89 19 HOH HOH A . C 2 HOH 19 90 20 HOH HOH A . C 2 HOH 20 91 21 HOH HOH A . C 2 HOH 21 92 22 HOH HOH A . C 2 HOH 22 93 23 HOH HOH A . C 2 HOH 23 94 24 HOH HOH A . C 2 HOH 24 95 25 HOH HOH A . C 2 HOH 25 96 26 HOH HOH A . C 2 HOH 26 97 27 HOH HOH A . C 2 HOH 27 98 28 HOH HOH A . C 2 HOH 28 99 29 HOH HOH A . C 2 HOH 29 100 30 HOH HOH A . C 2 HOH 30 101 31 HOH HOH A . C 2 HOH 31 102 32 HOH HOH A . C 2 HOH 32 103 33 HOH HOH A . C 2 HOH 33 104 34 HOH HOH A . C 2 HOH 34 105 35 HOH HOH A . C 2 HOH 35 106 36 HOH HOH A . C 2 HOH 36 107 37 HOH HOH A . C 2 HOH 37 108 108 HOH HOH A . C 2 HOH 38 109 109 HOH HOH A . C 2 HOH 39 110 38 HOH HOH A . C 2 HOH 40 111 111 HOH HOH A . C 2 HOH 41 112 39 HOH HOH A . C 2 HOH 42 113 40 HOH HOH A . C 2 HOH 43 114 114 HOH HOH A . C 2 HOH 44 115 90 HOH HOH A . C 2 HOH 45 116 41 HOH HOH A . C 2 HOH 46 117 42 HOH HOH A . C 2 HOH 47 118 118 HOH HOH A . C 2 HOH 48 119 43 HOH HOH A . C 2 HOH 49 120 44 HOH HOH A . C 2 HOH 50 121 121 HOH HOH A . C 2 HOH 51 122 45 HOH HOH A . C 2 HOH 52 123 47 HOH HOH A . C 2 HOH 53 124 48 HOH HOH A . C 2 HOH 54 125 49 HOH HOH A . C 2 HOH 55 126 55 HOH HOH A . C 2 HOH 56 127 112 HOH HOH A . C 2 HOH 57 128 66 HOH HOH A . D 2 HOH 1 84 84 HOH HOH B . D 2 HOH 2 85 85 HOH HOH B . D 2 HOH 3 86 50 HOH HOH B . D 2 HOH 4 87 87 HOH HOH B . D 2 HOH 5 88 88 HOH HOH B . D 2 HOH 6 89 89 HOH HOH B . D 2 HOH 7 91 91 HOH HOH B . D 2 HOH 8 92 92 HOH HOH B . D 2 HOH 9 93 93 HOH HOH B . D 2 HOH 10 94 94 HOH HOH B . D 2 HOH 11 95 95 HOH HOH B . D 2 HOH 12 96 96 HOH HOH B . D 2 HOH 13 97 97 HOH HOH B . D 2 HOH 14 98 98 HOH HOH B . D 2 HOH 15 99 99 HOH HOH B . D 2 HOH 16 100 100 HOH HOH B . D 2 HOH 17 101 101 HOH HOH B . D 2 HOH 18 102 102 HOH HOH B . D 2 HOH 19 103 103 HOH HOH B . D 2 HOH 20 104 51 HOH HOH B . D 2 HOH 21 105 105 HOH HOH B . D 2 HOH 22 106 106 HOH HOH B . D 2 HOH 23 107 107 HOH HOH B . D 2 HOH 24 108 52 HOH HOH B . D 2 HOH 25 109 53 HOH HOH B . D 2 HOH 26 110 54 HOH HOH B . D 2 HOH 27 111 56 HOH HOH B . D 2 HOH 28 113 113 HOH HOH B . D 2 HOH 29 114 57 HOH HOH B . D 2 HOH 30 115 115 HOH HOH B . D 2 HOH 31 116 59 HOH HOH B . D 2 HOH 32 117 117 HOH HOH B . D 2 HOH 33 118 60 HOH HOH B . D 2 HOH 34 119 61 HOH HOH B . D 2 HOH 35 120 62 HOH HOH B . D 2 HOH 36 121 63 HOH HOH B . D 2 HOH 37 122 64 HOH HOH B . D 2 HOH 38 123 65 HOH HOH B . D 2 HOH 39 124 58 HOH HOH B . D 2 HOH 40 125 67 HOH HOH B . D 2 HOH 41 126 68 HOH HOH B . D 2 HOH 42 127 69 HOH HOH B . D 2 HOH 43 128 70 HOH HOH B . D 2 HOH 44 129 71 HOH HOH B . D 2 HOH 45 130 72 HOH HOH B . D 2 HOH 46 131 73 HOH HOH B . D 2 HOH 47 132 74 HOH HOH B . D 2 HOH 48 133 75 HOH HOH B . D 2 HOH 49 134 76 HOH HOH B . D 2 HOH 50 135 77 HOH HOH B . D 2 HOH 51 136 78 HOH HOH B . D 2 HOH 52 137 79 HOH HOH B . D 2 HOH 53 138 81 HOH HOH B . D 2 HOH 54 139 82 HOH HOH B . D 2 HOH 55 140 83 HOH HOH B . # loop_ _pdbx_struct_mod_residue.id _pdbx_struct_mod_residue.label_asym_id _pdbx_struct_mod_residue.label_comp_id _pdbx_struct_mod_residue.label_seq_id _pdbx_struct_mod_residue.auth_asym_id _pdbx_struct_mod_residue.auth_comp_id _pdbx_struct_mod_residue.auth_seq_id _pdbx_struct_mod_residue.PDB_ins_code _pdbx_struct_mod_residue.parent_comp_id _pdbx_struct_mod_residue.details 1 A MSE 29 A MSE 42 ? MET SELENOMETHIONINE 2 A MSE 63 A MSE 76 ? MET SELENOMETHIONINE 3 B MSE 29 B MSE 42 ? MET SELENOMETHIONINE 4 B MSE 63 B MSE 76 ? MET SELENOMETHIONINE # loop_ _pdbx_struct_assembly.id _pdbx_struct_assembly.details _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count 1 software_defined_assembly PISA tetrameric 4 2 software_defined_assembly PISA dimeric 2 3 software_defined_assembly PISA dimeric 2 # loop_ _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression _pdbx_struct_assembly_gen.asym_id_list 1 1,2 A,B,C,D 2 1 A,B,C,D 3 1,2 B,D # loop_ _pdbx_struct_assembly_prop.biol_id _pdbx_struct_assembly_prop.type _pdbx_struct_assembly_prop.value _pdbx_struct_assembly_prop.details 1 'ABSA (A^2)' 4700 ? 1 MORE -33 ? 1 'SSA (A^2)' 13680 ? 2 'ABSA (A^2)' 1260 ? 2 MORE -8 ? 2 'SSA (A^2)' 7930 ? 3 'ABSA (A^2)' 1550 ? 3 MORE -13 ? 3 'SSA (A^2)' 8010 ? # 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_755 -x+2,-y,z -1.0000000000 0.0000000000 0.0000000000 108.3060000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 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 2009-03-31 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-04-04 4 'Structure model' 1 3 2018-01-24 5 'Structure model' 1 4 2022-04-13 # _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' 'Refinement description' 3 2 'Structure model' 'Version format compliance' 4 3 'Structure model' 'Structure summary' 5 4 'Structure model' 'Database references' 6 5 'Structure model' 'Database references' 7 5 'Structure model' 'Derived calculations' 8 5 '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 4 'Structure model' citation_author 2 5 'Structure model' audit_author 3 5 'Structure model' citation_author 4 5 'Structure model' database_2 5 5 'Structure model' struct_conn # 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 4 'Structure model' '_citation_author.name' 2 5 'Structure model' '_audit_author.identifier_ORCID' 3 5 'Structure model' '_citation_author.identifier_ORCID' 4 5 'Structure model' '_database_2.pdbx_DOI' 5 5 'Structure model' '_database_2.pdbx_database_accession' 6 5 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' # loop_ _pdbx_refine_tls.pdbx_refine_id _pdbx_refine_tls.id _pdbx_refine_tls.details _pdbx_refine_tls.method _pdbx_refine_tls.origin_x _pdbx_refine_tls.origin_y _pdbx_refine_tls.origin_z _pdbx_refine_tls.T[1][1] _pdbx_refine_tls.T[2][2] _pdbx_refine_tls.T[3][3] _pdbx_refine_tls.T[1][2] _pdbx_refine_tls.T[1][3] _pdbx_refine_tls.T[2][3] _pdbx_refine_tls.L[1][1] _pdbx_refine_tls.L[2][2] _pdbx_refine_tls.L[3][3] _pdbx_refine_tls.L[1][2] _pdbx_refine_tls.L[1][3] _pdbx_refine_tls.L[2][3] _pdbx_refine_tls.S[1][1] _pdbx_refine_tls.S[2][2] _pdbx_refine_tls.S[3][3] _pdbx_refine_tls.S[1][2] _pdbx_refine_tls.S[1][3] _pdbx_refine_tls.S[2][3] _pdbx_refine_tls.S[2][1] _pdbx_refine_tls.S[3][1] _pdbx_refine_tls.S[3][2] 'X-RAY DIFFRACTION' 1 ? refined 36.5240 9.3190 14.2800 0.1378 0.1288 0.1702 0.0945 0.0074 -0.0086 2.3579 0.7330 4.2875 0.6230 -1.3132 -0.4109 0.1162 0.0692 -0.1855 -0.0697 0.2915 0.0717 0.0423 -0.2888 -0.5035 'X-RAY DIFFRACTION' 2 ? refined 51.3140 8.4800 -2.3430 0.1256 0.0277 0.1461 -0.0040 0.0092 0.0296 1.6668 1.3447 1.9216 -0.8807 -0.9162 -0.0506 0.0351 0.0622 -0.0973 0.1152 0.3333 -0.0517 -0.0011 -0.2702 -0.1477 # loop_ _pdbx_refine_tls_group.pdbx_refine_id _pdbx_refine_tls_group.id _pdbx_refine_tls_group.refine_tls_id _pdbx_refine_tls_group.beg_auth_asym_id _pdbx_refine_tls_group.beg_auth_seq_id _pdbx_refine_tls_group.end_auth_asym_id _pdbx_refine_tls_group.end_auth_seq_id _pdbx_refine_tls_group.selection_details _pdbx_refine_tls_group.beg_label_asym_id _pdbx_refine_tls_group.beg_label_seq_id _pdbx_refine_tls_group.end_label_asym_id _pdbx_refine_tls_group.end_label_seq_id _pdbx_refine_tls_group.selection 'X-RAY DIFFRACTION' 1 1 A 14 A 83 ? . . . . ? 'X-RAY DIFFRACTION' 2 2 B 14 B 83 ? . . . . ? # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal Blu-Ice 'data collection' . ? 1 SOLVE phasing . ? 2 RESOLVE 'model building' . ? 3 REFMAC refinement 5.5.0062 ? 4 Coot 'model building' 0.3.3 ? 5 HKL-2000 'data reduction' . ? 6 HKL-2000 'data scaling' . ? 7 RESOLVE phasing . ? 8 # _pdbx_entry_details.entry_id 3GHD _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;AUTHORS STATE THAT THE PROTEIN WAS CRYSTALLIZED BY IN SITU PROTEOLYSIS METHOD AND THE EXACT SEQUENCE WENT INTO THE CRYSTAL WAS NOT DETERMINED. THE PROTEIN WAS MIXED WITH 100:1(W/W) WITH CHYMOTRYPSIN IMMEDIATELY PRIOR TO CRYSTALLIZATION TRIAL. THE FULL SEQUENCE BEFORE PROTEOLYSIS WAS MGSSHHHHHHSSGRENLYFQGMAQKILVEQVVKRKAIVVQPKDTVDRVAKILSRNKAG SAVVMEGDEILGVVTERDILDKVVAKGKNPKEVKVEEIMTKNPVKIEYDYDIEDVIEL MTEKGVRRVLVTKFGKPIGFVTAADILAALASHNHEEEEEEREEESEVYGICEVCGQY GALYKVYHEGRELWVCETCKDLIEGR ; _pdbx_entry_details.has_ligand_of_interest ? # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 NE _pdbx_validate_rmsd_angle.auth_asym_id_1 B _pdbx_validate_rmsd_angle.auth_comp_id_1 ARG _pdbx_validate_rmsd_angle.auth_seq_id_1 54 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CZ _pdbx_validate_rmsd_angle.auth_asym_id_2 B _pdbx_validate_rmsd_angle.auth_comp_id_2 ARG _pdbx_validate_rmsd_angle.auth_seq_id_2 54 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 NH1 _pdbx_validate_rmsd_angle.auth_asym_id_3 B _pdbx_validate_rmsd_angle.auth_comp_id_3 ARG _pdbx_validate_rmsd_angle.auth_seq_id_3 54 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 123.53 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation 3.23 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # 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 ASN A 79 ? ? -52.66 109.26 2 1 VAL B 60 ? ? -116.01 -71.24 # 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 21 ? CG ? A LYS 8 CG 2 1 Y 1 A LYS 21 ? CD ? A LYS 8 CD 3 1 Y 1 A LYS 21 ? CE ? A LYS 8 CE 4 1 Y 1 A LYS 21 ? NZ ? A LYS 8 NZ 5 1 Y 1 A ARG 26 ? NE ? A ARG 13 NE 6 1 Y 1 A ARG 26 ? CZ ? A ARG 13 CZ 7 1 Y 1 A ARG 26 ? NH1 ? A ARG 13 NH1 8 1 Y 1 A ARG 26 ? NH2 ? A ARG 13 NH2 9 1 Y 1 A LYS 29 ? CG ? A LYS 16 CG 10 1 Y 1 A LYS 29 ? CD ? A LYS 16 CD 11 1 Y 1 A LYS 29 ? CE ? A LYS 16 CE 12 1 Y 1 A LYS 29 ? NZ ? A LYS 16 NZ 13 1 Y 1 A ARG 33 ? NE ? A ARG 20 NE 14 1 Y 1 A ARG 33 ? CZ ? A ARG 20 CZ 15 1 Y 1 A ARG 33 ? NH1 ? A ARG 20 NH1 16 1 Y 1 A ARG 33 ? NH2 ? A ARG 20 NH2 17 1 Y 1 A LYS 35 ? CD ? A LYS 22 CD 18 1 Y 1 A LYS 35 ? CE ? A LYS 22 CE 19 1 Y 1 A LYS 35 ? NZ ? A LYS 22 NZ 20 1 Y 1 A LYS 78 ? CG ? A LYS 65 CG 21 1 Y 1 A LYS 78 ? CD ? A LYS 65 CD 22 1 Y 1 A LYS 78 ? CE ? A LYS 65 CE 23 1 Y 1 A LYS 78 ? NZ ? A LYS 65 NZ 24 1 Y 1 A LYS 82 ? CG ? A LYS 69 CG 25 1 Y 1 A LYS 82 ? CD ? A LYS 69 CD 26 1 Y 1 A LYS 82 ? CE ? A LYS 69 CE 27 1 Y 1 A LYS 82 ? NZ ? A LYS 69 NZ 28 1 Y 1 B ARG 26 ? CG ? B ARG 13 CG 29 1 Y 1 B ARG 26 ? CD ? B ARG 13 CD 30 1 Y 1 B ARG 26 ? NE ? B ARG 13 NE 31 1 Y 1 B ARG 26 ? CZ ? B ARG 13 CZ 32 1 Y 1 B ARG 26 ? NH1 ? B ARG 13 NH1 33 1 Y 1 B ARG 26 ? NH2 ? B ARG 13 NH2 34 1 Y 1 B GLU 46 ? OE1 ? B GLU 33 OE1 35 1 Y 1 B GLU 46 ? OE2 ? B GLU 33 OE2 36 1 Y 1 B LYS 71 ? CE ? B LYS 58 CE 37 1 Y 1 B LYS 71 ? NZ ? B LYS 58 NZ 38 1 Y 1 B LYS 78 ? CE ? B LYS 65 CE 39 1 Y 1 B LYS 78 ? NZ ? B LYS 65 NZ # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #