data_2RFF # _entry.id 2RFF # _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 2RFF pdb_00002rff 10.2210/pdb2rff/pdb RCSB RCSB044792 ? ? WWPDB D_1000044792 ? ? # _pdbx_database_related.db_name TargetDB _pdbx_database_related.db_id 376473 _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.SG_entry Y _pdbx_database_status.entry_id 2RFF _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2007-09-28 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_cs ? _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 a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 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 2RFF _cell.length_a 25.007 _cell.length_b 29.884 _cell.length_c 35.202 _cell.angle_alpha 77.240 _cell.angle_beta 73.720 _cell.angle_gamma 78.300 _cell.pdbx_unique_axis ? _cell.Z_PDB 1 _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 2RFF _symmetry.Int_Tables_number 1 _symmetry.space_group_name_H-M 'P 1' _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 nucleotidyltransferase' 13133.482 1 ? ? ? ? 2 non-polymer syn 1,2-ETHANEDIOL 62.068 2 ? ? ? ? 3 water nat water 18.015 107 ? ? ? ? # _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)GKGKSAIESQIR(MSE)LKLAKEIVEEVASSFPNLEEVYIFGSRARGDYLDTSDIDILFVFKGIKE(MSE)NVF DR(MSE)Y(MSE)VSRFIRGNVDYIVLDEGEKDRVKDKVLFWKREKGFVLL ; _entity_poly.pdbx_seq_one_letter_code_can ;GMGKGKSAIESQIRMLKLAKEIVEEVASSFPNLEEVYIFGSRARGDYLDTSDIDILFVFKGIKEMNVFDRMYMVSRFIRG NVDYIVLDEGEKDRVKDKVLFWKREKGFVLL ; _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier 376473 # 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 GLY n 1 4 LYS n 1 5 GLY n 1 6 LYS n 1 7 SER n 1 8 ALA n 1 9 ILE n 1 10 GLU n 1 11 SER n 1 12 GLN n 1 13 ILE n 1 14 ARG n 1 15 MSE n 1 16 LEU n 1 17 LYS n 1 18 LEU n 1 19 ALA n 1 20 LYS n 1 21 GLU n 1 22 ILE n 1 23 VAL n 1 24 GLU n 1 25 GLU n 1 26 VAL n 1 27 ALA n 1 28 SER n 1 29 SER n 1 30 PHE n 1 31 PRO n 1 32 ASN n 1 33 LEU n 1 34 GLU n 1 35 GLU n 1 36 VAL n 1 37 TYR n 1 38 ILE n 1 39 PHE n 1 40 GLY n 1 41 SER n 1 42 ARG n 1 43 ALA n 1 44 ARG n 1 45 GLY n 1 46 ASP n 1 47 TYR n 1 48 LEU n 1 49 ASP n 1 50 THR n 1 51 SER n 1 52 ASP n 1 53 ILE n 1 54 ASP n 1 55 ILE n 1 56 LEU n 1 57 PHE n 1 58 VAL n 1 59 PHE n 1 60 LYS n 1 61 GLY n 1 62 ILE n 1 63 LYS n 1 64 GLU n 1 65 MSE n 1 66 ASN n 1 67 VAL n 1 68 PHE n 1 69 ASP n 1 70 ARG n 1 71 MSE n 1 72 TYR n 1 73 MSE n 1 74 VAL n 1 75 SER n 1 76 ARG n 1 77 PHE n 1 78 ILE n 1 79 ARG n 1 80 GLY n 1 81 ASN n 1 82 VAL n 1 83 ASP n 1 84 TYR n 1 85 ILE n 1 86 VAL n 1 87 LEU n 1 88 ASP n 1 89 GLU n 1 90 GLY n 1 91 GLU n 1 92 LYS n 1 93 ASP n 1 94 ARG n 1 95 VAL n 1 96 LYS n 1 97 ASP n 1 98 LYS n 1 99 VAL n 1 100 LEU n 1 101 PHE n 1 102 TRP n 1 103 LYS n 1 104 ARG n 1 105 GLU n 1 106 LYS n 1 107 GLY n 1 108 PHE n 1 109 VAL n 1 110 LEU n 1 111 LEU n # _entity_src_gen.entity_id 1 _entity_src_gen.pdbx_src_id 1 _entity_src_gen.pdbx_alt_source_flag sample _entity_src_gen.pdbx_seq_type ? _entity_src_gen.pdbx_beg_seq_num ? _entity_src_gen.pdbx_end_seq_num ? _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus Sulfolobus _entity_src_gen.pdbx_gene_src_gene 'NP_343093.1, SSO1673' _entity_src_gen.gene_src_species 'Sulfolobus solfataricus' _entity_src_gen.gene_src_strain 'P2, DSM 1617, JCM 11322' _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 'Sulfolobus solfataricus P2' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 273057 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc 35092 _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 Escherichia _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 Q97XP0_SULSO _struct_ref.pdbx_db_accession Q97XP0 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code ;MGKGKSAIESQIRMLKLAKEIVEEVASSFPNLEEVYIFGSRARGDYLDTSDIDILFVFKGIKEMNVFDRMYMVSRFIRGN VDYIVLDEGEKDRVKDKVLFWKREKGFVLL ; _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 2RFF _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 111 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q97XP0 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 110 _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 110 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2RFF _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 Q97XP0 _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 EDO non-polymer . 1,2-ETHANEDIOL 'ETHYLENE GLYCOL' 'C2 H6 O2' 62.068 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 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.method 'X-RAY DIFFRACTION' _exptl.entry_id 2RFF # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 1.85 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 33.65 _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 'NANODROP, 20.0% PEG MME2000, 0.1M Tris-HCl pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K' _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 300 mm CCD' _diffrn_detector.details 'Adjustable focusing mirrors in K-B geometry' _diffrn_detector.pdbx_collection_date 2007-08-19 # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'Si(111) Double crystal' _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 0.95373 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.pdbx_synchrotron_beamline 23-ID-D _diffrn_source.type 'APS BEAMLINE 23-ID-D' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 0.95373 _diffrn_source.pdbx_synchrotron_site APS # _reflns.entry_id 2RFF _reflns.d_resolution_high 1.40 _reflns.d_resolution_low 33.278 _reflns.number_obs 16758 _reflns.pdbx_Rmerge_I_obs 0.064 _reflns.pdbx_netI_over_sigmaI 13.000 _reflns.pdbx_chi_squared 1.274 _reflns.pdbx_redundancy 3.700 _reflns.percent_possible_obs 90.500 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_diffrn_id _reflns_shell.pdbx_ordinal 1.40 1.45 ? ? ? 0.261 ? ? 1.858 3.00 ? 1000 54.00 ? 1 1.45 1.51 ? ? ? 0.225 ? ? 1.622 3.20 ? 1443 78.00 ? 2 1.51 1.58 ? ? ? 0.203 ? ? 1.371 3.60 ? 1780 94.30 ? 3 1.58 1.66 ? ? ? 0.174 ? ? 1.306 3.80 ? 1761 95.10 ? 4 1.66 1.76 ? ? ? 0.134 ? ? 1.138 3.90 ? 1761 96.00 ? 5 1.76 1.90 ? ? ? 0.101 ? ? 1.101 3.90 ? 1766 96.70 ? 6 1.90 2.09 ? ? ? 0.081 ? ? 1.212 3.90 ? 1795 96.70 ? 7 2.09 2.39 ? ? ? 0.067 ? ? 1.286 3.90 ? 1799 97.30 ? 8 2.39 3.02 ? ? ? 0.060 ? ? 1.333 3.90 ? 1818 98.00 ? 9 3.02 33.278 ? ? ? 0.046 ? ? 1.017 3.90 ? 1835 99.00 ? 10 # _refine.entry_id 2RFF _refine.ls_d_res_high 1.400 _refine.ls_d_res_low 33.278 _refine.pdbx_ls_sigma_F 0.00 _refine.ls_percent_reflns_obs 90.500 _refine.ls_number_reflns_obs 16755 _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. 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. 3. EDO MOLECULES FROM THE CRYO SOLUTION ARE MODELED. ; _refine.ls_R_factor_obs 0.147 _refine.ls_R_factor_R_work 0.145 _refine.ls_R_factor_R_free 0.187 _refine.ls_percent_reflns_R_free 5.100 _refine.ls_number_reflns_R_free 851 _refine.B_iso_mean 13.191 _refine.aniso_B[1][1] -1.830 _refine.aniso_B[2][2] -0.480 _refine.aniso_B[3][3] 3.090 _refine.aniso_B[1][2] 0.680 _refine.aniso_B[1][3] -0.200 _refine.aniso_B[2][3] -2.130 _refine.correlation_coeff_Fo_to_Fc 0.977 _refine.correlation_coeff_Fo_to_Fc_free 0.959 _refine.pdbx_overall_ESU_R 0.092 _refine.pdbx_overall_ESU_R_Free 0.073 _refine.overall_SU_ML 0.067 _refine.overall_SU_B 3.929 _refine.solvent_model_details 'BABINET MODEL WITH 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.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_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_phase_error ? _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 990 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 8 _refine_hist.number_atoms_solvent 107 _refine_hist.number_atoms_total 1105 _refine_hist.d_res_high 1.400 _refine_hist.d_res_low 33.278 # 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 1026 0.017 0.022 ? 'X-RAY DIFFRACTION' ? r_bond_other_d 757 0.005 0.020 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1387 1.807 1.987 ? 'X-RAY DIFFRACTION' ? r_angle_other_deg 1852 1.429 3.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 140 4.859 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 50 22.395 23.800 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 218 10.880 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 9 12.724 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 149 0.108 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 1149 0.007 0.020 ? 'X-RAY DIFFRACTION' ? r_gen_planes_other 223 0.003 0.020 ? 'X-RAY DIFFRACTION' ? r_nbd_refined 172 0.228 0.200 ? 'X-RAY DIFFRACTION' ? r_nbd_other 792 0.160 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 484 0.166 0.200 ? 'X-RAY DIFFRACTION' ? r_nbtor_other 554 0.073 0.200 ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 71 0.111 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 11 0.177 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 51 0.151 0.200 ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 22 0.146 0.200 ? 'X-RAY DIFFRACTION' ? r_mcbond_it 692 2.459 2.000 ? 'X-RAY DIFFRACTION' ? r_mcbond_other 247 1.218 2.000 ? 'X-RAY DIFFRACTION' ? r_mcangle_it 984 3.056 4.000 ? 'X-RAY DIFFRACTION' ? r_scbond_it 472 3.566 4.000 ? 'X-RAY DIFFRACTION' ? r_scangle_it 389 4.508 6.000 ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr 2069 1.592 3.000 ? 'X-RAY DIFFRACTION' ? r_sphericity_free 107 6.787 3.000 ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded 1755 4.292 3.000 ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.d_res_high 1.40 _refine_ls_shell.d_res_low 1.44 _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.percent_reflns_obs 51.350 _refine_ls_shell.number_reflns_R_work 674 _refine_ls_shell.R_factor_all ? _refine_ls_shell.R_factor_R_work 0.214 _refine_ls_shell.R_factor_R_free 0.293 _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 31 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.number_reflns_all 705 _refine_ls_shell.number_reflns_obs ? _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' # _struct.entry_id 2RFF _struct.title 'Crystal structure of a putative nucleotidyltransferase (NP_343093.1) from Sulfolobus solfataricus at 1.40 A resolution' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.text ;NP_343093.1, A Putative Nucleotidyltransferase, Nucleotidyltransferase domain, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, TRANSFERASE ; _struct_keywords.pdbx_keywords TRANSFERASE _struct_keywords.entry_id 2RFF # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? D N N 3 ? # _struct_biol.id 1 _struct_biol.details ;CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. ; # 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 GLY A 5 ? PHE A 30 ? GLY A 4 PHE A 29 1 ? 26 HELX_P HELX_P2 2 GLY A 40 ? GLY A 45 ? GLY A 39 GLY A 44 1 ? 6 HELX_P HELX_P3 3 ASN A 66 ? SER A 75 ? ASN A 65 SER A 74 1 ? 10 HELX_P HELX_P4 4 ARG A 76 ? ILE A 78 ? ARG A 75 ILE A 77 5 ? 3 HELX_P HELX_P5 5 GLY A 90 ? VAL A 95 ? GLY A 89 VAL A 94 5 ? 6 # _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 GLY 1 C ? ? ? 1_555 A MSE 2 N ? ? A GLY 0 A MSE 1 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale2 covale both ? A MSE 2 C ? ? ? 1_555 A GLY 3 N ? ? A MSE 1 A GLY 2 1_555 ? ? ? ? ? ? ? 1.335 ? ? covale3 covale both ? A ARG 14 C ? ? ? 1_555 A MSE 15 N ? ? A ARG 13 A MSE 14 1_555 ? ? ? ? ? ? ? 1.329 ? ? covale4 covale both ? A MSE 15 C ? ? ? 1_555 A LEU 16 N ? ? A MSE 14 A LEU 15 1_555 ? ? ? ? ? ? ? 1.314 ? ? covale5 covale both ? A GLU 64 C ? ? ? 1_555 A MSE 65 N ? ? A GLU 63 A MSE 64 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale6 covale both ? A MSE 65 C ? ? ? 1_555 A ASN 66 N ? ? A MSE 64 A ASN 65 1_555 ? ? ? ? ? ? ? 1.336 ? ? covale7 covale both ? A ARG 70 C ? ? ? 1_555 A MSE 71 N ? ? A ARG 69 A MSE 70 1_555 ? ? ? ? ? ? ? 1.324 ? ? covale8 covale both ? A MSE 71 C ? ? ? 1_555 A TYR 72 N ? ? A MSE 70 A TYR 71 1_555 ? ? ? ? ? ? ? 1.339 ? ? covale9 covale both ? A TYR 72 C ? ? ? 1_555 A MSE 73 N ? ? A TYR 71 A MSE 72 1_555 ? ? ? ? ? ? ? 1.351 ? ? covale10 covale both ? A MSE 73 C ? ? ? 1_555 A VAL 74 N ? ? A MSE 72 A VAL 73 1_555 ? ? ? ? ? ? ? 1.330 ? ? # _struct_conn_type.id covale _struct_conn_type.criteria ? _struct_conn_type.reference ? # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 5 _struct_sheet.details ? # 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 A 4 5 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 VAL A 82 ? ASP A 88 ? VAL A 81 ASP A 87 A 2 ILE A 53 ? PHE A 59 ? ILE A 52 PHE A 58 A 3 LEU A 33 ? PHE A 39 ? LEU A 32 PHE A 38 A 4 LYS A 98 ? LYS A 103 ? LYS A 97 LYS A 102 A 5 GLY A 107 ? PHE A 108 ? GLY A 106 PHE A 107 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id A 1 2 O ILE A 85 ? O ILE A 84 N PHE A 57 ? N PHE A 56 A 2 3 O LEU A 56 ? O LEU A 55 N TYR A 37 ? N TYR A 36 A 3 4 N ILE A 38 ? N ILE A 37 O VAL A 99 ? O VAL A 98 A 4 5 N LYS A 103 ? N LYS A 102 O GLY A 107 ? O GLY A 106 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A EDO 111 ? 4 'BINDING SITE FOR RESIDUE EDO A 111' AC2 Software A EDO 112 ? 6 'BINDING SITE FOR RESIDUE EDO A 112' # 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 4 ARG A 94 ? ARG A 93 . ? 1_655 ? 2 AC1 4 GLU A 105 ? GLU A 104 . ? 1_555 ? 3 AC1 4 HOH D . ? HOH A 140 . ? 1_555 ? 4 AC1 4 HOH D . ? HOH A 195 . ? 1_555 ? 5 AC2 6 MSE A 71 ? MSE A 70 . ? 1_555 ? 6 AC2 6 ASP A 83 ? ASP A 82 . ? 1_555 ? 7 AC2 6 TYR A 84 ? TYR A 83 . ? 1_555 ? 8 AC2 6 ARG A 104 ? ARG A 103 . ? 1_455 ? 9 AC2 6 HOH D . ? HOH A 115 . ? 1_455 ? 10 AC2 6 HOH D . ? HOH A 129 . ? 1_455 ? # _atom_sites.entry_id 2RFF _atom_sites.fract_transf_matrix[1][1] 0.039989 _atom_sites.fract_transf_matrix[1][2] -0.008284 _atom_sites.fract_transf_matrix[1][3] -0.010389 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.034173 _atom_sites.fract_transf_matrix[2][3] -0.006059 _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] 0.030055 _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 0 GLY GLY A . n A 1 2 MSE 2 1 1 MSE MSE A . n A 1 3 GLY 3 2 2 GLY GLY A . n A 1 4 LYS 4 3 3 LYS LYS A . n A 1 5 GLY 5 4 4 GLY GLY A . n A 1 6 LYS 6 5 5 LYS LYS A . n A 1 7 SER 7 6 6 SER SER A . n A 1 8 ALA 8 7 7 ALA ALA A . n A 1 9 ILE 9 8 8 ILE ILE A . n A 1 10 GLU 10 9 9 GLU GLU A . n A 1 11 SER 11 10 10 SER SER A . n A 1 12 GLN 12 11 11 GLN GLN A . n A 1 13 ILE 13 12 12 ILE ILE A . n A 1 14 ARG 14 13 13 ARG ARG A . n A 1 15 MSE 15 14 14 MSE MSE A . n A 1 16 LEU 16 15 15 LEU LEU A . n A 1 17 LYS 17 16 16 LYS LYS A . n A 1 18 LEU 18 17 17 LEU LEU A . n A 1 19 ALA 19 18 18 ALA ALA A . n A 1 20 LYS 20 19 19 LYS LYS A . n A 1 21 GLU 21 20 20 GLU GLU A . n A 1 22 ILE 22 21 21 ILE ILE A . n A 1 23 VAL 23 22 22 VAL VAL A . n A 1 24 GLU 24 23 23 GLU GLU A . n A 1 25 GLU 25 24 24 GLU GLU A . n A 1 26 VAL 26 25 25 VAL VAL A . n A 1 27 ALA 27 26 26 ALA ALA A . n A 1 28 SER 28 27 27 SER SER A . n A 1 29 SER 29 28 28 SER SER A . n A 1 30 PHE 30 29 29 PHE PHE A . n A 1 31 PRO 31 30 30 PRO PRO A . n A 1 32 ASN 32 31 31 ASN ASN A . n A 1 33 LEU 33 32 32 LEU LEU A . n A 1 34 GLU 34 33 33 GLU GLU A . n A 1 35 GLU 35 34 34 GLU GLU A . n A 1 36 VAL 36 35 35 VAL VAL A . n A 1 37 TYR 37 36 36 TYR TYR A . n A 1 38 ILE 38 37 37 ILE ILE A . n A 1 39 PHE 39 38 38 PHE PHE A . n A 1 40 GLY 40 39 39 GLY GLY A . n A 1 41 SER 41 40 40 SER SER A . n A 1 42 ARG 42 41 41 ARG ARG A . n A 1 43 ALA 43 42 42 ALA ALA A . n A 1 44 ARG 44 43 43 ARG ARG A . n A 1 45 GLY 45 44 44 GLY GLY A . n A 1 46 ASP 46 45 45 ASP ASP A . n A 1 47 TYR 47 46 46 TYR TYR A . n A 1 48 LEU 48 47 47 LEU LEU A . n A 1 49 ASP 49 48 48 ASP ASP A . n A 1 50 THR 50 49 49 THR THR A . n A 1 51 SER 51 50 50 SER SER A . n A 1 52 ASP 52 51 51 ASP ASP A . n A 1 53 ILE 53 52 52 ILE ILE A . n A 1 54 ASP 54 53 53 ASP ASP A . n A 1 55 ILE 55 54 54 ILE ILE A . n A 1 56 LEU 56 55 55 LEU LEU A . n A 1 57 PHE 57 56 56 PHE PHE A . n A 1 58 VAL 58 57 57 VAL VAL A . n A 1 59 PHE 59 58 58 PHE PHE A . n A 1 60 LYS 60 59 59 LYS LYS A . n A 1 61 GLY 61 60 60 GLY GLY A . n A 1 62 ILE 62 61 61 ILE ILE A . n A 1 63 LYS 63 62 62 LYS LYS A . n A 1 64 GLU 64 63 63 GLU GLU A . n A 1 65 MSE 65 64 64 MSE MSE A . n A 1 66 ASN 66 65 65 ASN ASN A . n A 1 67 VAL 67 66 66 VAL VAL A . n A 1 68 PHE 68 67 67 PHE PHE A . n A 1 69 ASP 69 68 68 ASP ASP A . n A 1 70 ARG 70 69 69 ARG ARG A . n A 1 71 MSE 71 70 70 MSE MSE A . n A 1 72 TYR 72 71 71 TYR TYR A . n A 1 73 MSE 73 72 72 MSE MSE A . n A 1 74 VAL 74 73 73 VAL VAL A . n A 1 75 SER 75 74 74 SER SER A . n A 1 76 ARG 76 75 75 ARG ARG A . n A 1 77 PHE 77 76 76 PHE PHE A . n A 1 78 ILE 78 77 77 ILE ILE A . n A 1 79 ARG 79 78 78 ARG ARG A . n A 1 80 GLY 80 79 79 GLY GLY A . n A 1 81 ASN 81 80 80 ASN ASN A . n A 1 82 VAL 82 81 81 VAL VAL A . n A 1 83 ASP 83 82 82 ASP ASP A . n A 1 84 TYR 84 83 83 TYR TYR A . n A 1 85 ILE 85 84 84 ILE ILE A . n A 1 86 VAL 86 85 85 VAL VAL A . n A 1 87 LEU 87 86 86 LEU LEU A . n A 1 88 ASP 88 87 87 ASP ASP A . n A 1 89 GLU 89 88 88 GLU GLU A . n A 1 90 GLY 90 89 89 GLY GLY A . n A 1 91 GLU 91 90 90 GLU GLU A . n A 1 92 LYS 92 91 91 LYS LYS A . n A 1 93 ASP 93 92 92 ASP ASP A . n A 1 94 ARG 94 93 93 ARG ARG A . n A 1 95 VAL 95 94 94 VAL VAL A . n A 1 96 LYS 96 95 95 LYS LYS A . n A 1 97 ASP 97 96 96 ASP ASP A . n A 1 98 LYS 98 97 97 LYS LYS A . n A 1 99 VAL 99 98 98 VAL VAL A . n A 1 100 LEU 100 99 99 LEU LEU A . n A 1 101 PHE 101 100 100 PHE PHE A . n A 1 102 TRP 102 101 101 TRP TRP A . n A 1 103 LYS 103 102 102 LYS LYS A . n A 1 104 ARG 104 103 103 ARG ARG A . n A 1 105 GLU 105 104 104 GLU GLU A . n A 1 106 LYS 106 105 105 LYS LYS A . n A 1 107 GLY 107 106 106 GLY GLY A . n A 1 108 PHE 108 107 107 PHE PHE A . n A 1 109 VAL 109 108 108 VAL VAL A . n A 1 110 LEU 110 109 109 LEU LEU A . n A 1 111 LEU 111 110 110 LEU LEU 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 EDO 1 111 1 EDO EDO A . C 2 EDO 1 112 2 EDO EDO A . D 3 HOH 1 113 3 HOH HOH A . D 3 HOH 2 114 4 HOH HOH A . D 3 HOH 3 115 5 HOH HOH A . D 3 HOH 4 116 6 HOH HOH A . D 3 HOH 5 117 7 HOH HOH A . D 3 HOH 6 118 8 HOH HOH A . D 3 HOH 7 119 9 HOH HOH A . D 3 HOH 8 120 10 HOH HOH A . D 3 HOH 9 121 11 HOH HOH A . D 3 HOH 10 122 12 HOH HOH A . D 3 HOH 11 123 13 HOH HOH A . D 3 HOH 12 124 14 HOH HOH A . D 3 HOH 13 125 15 HOH HOH A . D 3 HOH 14 126 16 HOH HOH A . D 3 HOH 15 127 17 HOH HOH A . D 3 HOH 16 128 18 HOH HOH A . D 3 HOH 17 129 19 HOH HOH A . D 3 HOH 18 130 20 HOH HOH A . D 3 HOH 19 131 21 HOH HOH A . D 3 HOH 20 132 22 HOH HOH A . D 3 HOH 21 133 23 HOH HOH A . D 3 HOH 22 134 24 HOH HOH A . D 3 HOH 23 135 25 HOH HOH A . D 3 HOH 24 136 26 HOH HOH A . D 3 HOH 25 137 27 HOH HOH A . D 3 HOH 26 138 28 HOH HOH A . D 3 HOH 27 139 29 HOH HOH A . D 3 HOH 28 140 30 HOH HOH A . D 3 HOH 29 141 31 HOH HOH A . D 3 HOH 30 142 32 HOH HOH A . D 3 HOH 31 143 33 HOH HOH A . D 3 HOH 32 144 34 HOH HOH A . D 3 HOH 33 145 35 HOH HOH A . D 3 HOH 34 146 36 HOH HOH A . D 3 HOH 35 147 37 HOH HOH A . D 3 HOH 36 148 38 HOH HOH A . D 3 HOH 37 149 39 HOH HOH A . D 3 HOH 38 150 40 HOH HOH A . D 3 HOH 39 151 41 HOH HOH A . D 3 HOH 40 152 42 HOH HOH A . D 3 HOH 41 153 43 HOH HOH A . D 3 HOH 42 154 44 HOH HOH A . D 3 HOH 43 155 45 HOH HOH A . D 3 HOH 44 156 46 HOH HOH A . D 3 HOH 45 157 47 HOH HOH A . D 3 HOH 46 158 48 HOH HOH A . D 3 HOH 47 159 49 HOH HOH A . D 3 HOH 48 160 50 HOH HOH A . D 3 HOH 49 161 51 HOH HOH A . D 3 HOH 50 162 52 HOH HOH A . D 3 HOH 51 163 53 HOH HOH A . D 3 HOH 52 164 54 HOH HOH A . D 3 HOH 53 165 55 HOH HOH A . D 3 HOH 54 166 56 HOH HOH A . D 3 HOH 55 167 57 HOH HOH A . D 3 HOH 56 168 58 HOH HOH A . D 3 HOH 57 169 59 HOH HOH A . D 3 HOH 58 170 60 HOH HOH A . D 3 HOH 59 171 61 HOH HOH A . D 3 HOH 60 172 62 HOH HOH A . D 3 HOH 61 173 63 HOH HOH A . D 3 HOH 62 174 64 HOH HOH A . D 3 HOH 63 175 65 HOH HOH A . D 3 HOH 64 176 66 HOH HOH A . D 3 HOH 65 177 67 HOH HOH A . D 3 HOH 66 178 68 HOH HOH A . D 3 HOH 67 179 69 HOH HOH A . D 3 HOH 68 180 70 HOH HOH A . D 3 HOH 69 181 71 HOH HOH A . D 3 HOH 70 182 72 HOH HOH A . D 3 HOH 71 183 73 HOH HOH A . D 3 HOH 72 184 74 HOH HOH A . D 3 HOH 73 185 75 HOH HOH A . D 3 HOH 74 186 76 HOH HOH A . D 3 HOH 75 187 77 HOH HOH A . D 3 HOH 76 188 78 HOH HOH A . D 3 HOH 77 189 79 HOH HOH A . D 3 HOH 78 190 80 HOH HOH A . D 3 HOH 79 191 81 HOH HOH A . D 3 HOH 80 192 82 HOH HOH A . D 3 HOH 81 193 83 HOH HOH A . D 3 HOH 82 194 84 HOH HOH A . D 3 HOH 83 195 85 HOH HOH A . D 3 HOH 84 196 86 HOH HOH A . D 3 HOH 85 197 87 HOH HOH A . D 3 HOH 86 198 88 HOH HOH A . D 3 HOH 87 199 89 HOH HOH A . D 3 HOH 88 200 90 HOH HOH A . D 3 HOH 89 201 91 HOH HOH A . D 3 HOH 90 202 92 HOH HOH A . D 3 HOH 91 203 93 HOH HOH A . D 3 HOH 92 204 94 HOH HOH A . D 3 HOH 93 205 95 HOH HOH A . D 3 HOH 94 206 96 HOH HOH A . D 3 HOH 95 207 97 HOH HOH A . D 3 HOH 96 208 98 HOH HOH A . D 3 HOH 97 209 99 HOH HOH A . D 3 HOH 98 210 100 HOH HOH A . D 3 HOH 99 211 101 HOH HOH A . D 3 HOH 100 212 102 HOH HOH A . D 3 HOH 101 213 103 HOH HOH A . D 3 HOH 102 214 104 HOH HOH A . D 3 HOH 103 215 105 HOH HOH A . D 3 HOH 104 216 106 HOH HOH A . D 3 HOH 105 217 107 HOH HOH A . D 3 HOH 106 218 108 HOH HOH A . D 3 HOH 107 219 109 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 15 A MSE 14 ? MET SELENOMETHIONINE 3 A MSE 65 A MSE 64 ? MET SELENOMETHIONINE 4 A MSE 71 A MSE 70 ? MET SELENOMETHIONINE 5 A MSE 73 A MSE 72 ? 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 monomeric _pdbx_struct_assembly.oligomeric_count 1 # _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 # _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 2007-10-16 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 2023-01-25 # _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' 'Version format compliance' 2 3 'Structure model' 'Refinement description' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Derived calculations' 5 4 'Structure model' 'Refinement description' 6 5 'Structure model' 'Database references' 7 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' # _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 5.3.0040 ? 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 SCALEPACK . ? package 'Zbyszek Otwinowski' zbyszek@mix.swmed.edu 'data scaling' http://www.lnls.br/infra/linhasluz/denzo-hkl.htm ? ? 5 PDB_EXTRACT 3.000 'July 2, 2007' package PDB sw-help@rcsb.rutgers.edu 'data extraction' http://pdb.rutgers.edu/software/ C++ ? 6 MAR345 CCD ? ? ? ? 'data collection' ? ? ? 7 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 8 SOLVE . ? ? ? ? phasing ? ? ? 9 SHELXD . ? ? ? ? phasing ? ? ? 10 # loop_ _pdbx_database_remark.id _pdbx_database_remark.text 300 ; BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. CRYSTAL PACKING ANALYSIS SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. ; 999 ; SEQUENCE 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. ; # _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 A _pdbx_validate_rmsd_angle.auth_comp_id_1 ARG _pdbx_validate_rmsd_angle.auth_seq_id_1 13 _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 A _pdbx_validate_rmsd_angle.auth_comp_id_2 ARG _pdbx_validate_rmsd_angle.auth_seq_id_2 13 _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 A _pdbx_validate_rmsd_angle.auth_comp_id_3 ARG _pdbx_validate_rmsd_angle.auth_seq_id_3 13 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 124.23 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation 3.93 _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 MSE A 1 ? ? -41.13 85.61 2 1 MSE A 1 ? ? -37.58 82.57 3 1 ASP A 45 ? ? -88.05 36.03 4 1 ASP A 96 ? A 47.74 77.75 # 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 62 ? CD ? A LYS 63 CD 2 1 Y 1 A LYS 62 ? CE ? A LYS 63 CE 3 1 Y 1 A LYS 62 ? NZ ? A LYS 63 NZ 4 1 Y 1 A LYS 95 ? CE ? A LYS 96 CE 5 1 Y 1 A LYS 95 ? NZ ? A LYS 96 NZ # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 1,2-ETHANEDIOL EDO 3 water HOH #