data_1LJO # _entry.id 1LJO # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.286 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 1LJO RCSB RCSB016002 WWPDB D_1000016002 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.details _pdbx_database_related.content_type PDB 1D3B ;Crystal Structure Of The D3b Subcomplex Of The Human Core Snrnp Domain At 2.0a Resolution ; unspecified PDB 1B34 'Crystal Structure Of The D1d2 Sub-Complex From The Human Snrnp Core Domain' unspecified PDB 1I81 ;Crystal Structure Of A Heptameric Lsm Protein From Methanobacterium Thermoautotrophicum ; unspecified PDB 1I8F ;The Crystal Structure Of A Heptameric Archaeal Sm Protein: Implications For The Eukaryotic Snrnp Core ; unspecified PDB 1I5L ;Crystal Structure Of An Sm-Like Protein (Af-Sm1) From Archaeoglobus Fulgidus Complexed With Short Poly-U Rna ; unspecified PDB 1I4K ;Crystal Structure Of An Sm-Like Protein (Af-Sm1) From Archaeoglobus Fulgidus At 2.5a Resolution ; unspecified PDB 1JRI ;The Crystal Structure Of An Sm-Like Archaeal Protein With Two Heptamers In The Asymmetric Unit. ; unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 1LJO _pdbx_database_status.recvd_initial_deposition_date 2002-04-22 _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.SG_entry . _pdbx_database_status.status_code_sf REL _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_mr ? _pdbx_database_status.status_code_cs ? _pdbx_database_status.methods_development_category ? # loop_ _audit_author.name _audit_author.pdbx_ordinal 'Toro, I.' 1 'Basquin, J.' 2 'Teo-Dreher, H.' 3 'Suck, D.' 4 # loop_ _citation.id _citation.title _citation.journal_abbrev _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 _citation.book_publisher _citation.pdbx_database_id_PubMed _citation.pdbx_database_id_DOI primary ;Archaeal Sm proteins form heptameric and hexameric complexes: crystal structures of the Sm1 and Sm2 proteins from the hyperthermophile Archaeoglobus fulgidus. ; J.Mol.Biol. 320 129 142 2002 JMOBAK UK 0022-2836 0070 ? 12079339 '10.1016/S0022-2836(02)00406-0' 1 'RNA binding in an Sm core domain: X-ray structure and functional analysis of an archaeal Sm protein complex.' 'Embo J.' 20 2293 2303 2001 EMJODG UK 0261-4189 0897 ? ? 10.1093/emboj/20.9.2293 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Toro, I.' 1 primary 'Basquin, J.' 2 primary 'Teo-Dreher, H.' 3 primary 'Suck, D.' 4 1 'Toro, I.' 5 1 'Thore, S.' 6 1 'Mayer, C.' 7 1 'Basquin, J.' 8 1 'Sraphin, B.' 9 1 'Suck, D.' 10 # _cell.entry_id 1LJO _cell.length_a 58.420 _cell.length_b 58.420 _cell.length_c 32.084 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 120.00 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1LJO _symmetry.space_group_name_H-M 'P 6' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 168 # 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 'Archaeal Sm-like protein AF-Sm2' 8617.045 1 ? ;'N-terminal GA added' ; ? ? 2 non-polymer syn 'CADMIUM ION' 112.411 1 ? ? ? ? 3 non-polymer syn 'ACETIC ACID' 60.052 3 ? ? ? ? 4 water nat water 18.015 33 ? ? ? ? # _entity_poly.entity_id 1 _entity_poly.type 'polypeptide(L)' _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no _entity_poly.pdbx_seq_one_letter_code GAMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE _entity_poly.pdbx_seq_one_letter_code_can GAMVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE _entity_poly.pdbx_strand_id A _entity_poly.pdbx_target_identifier ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 GLY n 1 2 ALA n 1 3 MET n 1 4 VAL n 1 5 LEU n 1 6 PRO n 1 7 ASN n 1 8 GLN n 1 9 MET n 1 10 VAL n 1 11 LYS n 1 12 SER n 1 13 MET n 1 14 VAL n 1 15 GLY n 1 16 LYS n 1 17 ILE n 1 18 ILE n 1 19 ARG n 1 20 VAL n 1 21 GLU n 1 22 MET n 1 23 LYS n 1 24 GLY n 1 25 GLU n 1 26 GLU n 1 27 ASN n 1 28 GLN n 1 29 LEU n 1 30 VAL n 1 31 GLY n 1 32 LYS n 1 33 LEU n 1 34 GLU n 1 35 GLY n 1 36 VAL n 1 37 ASP n 1 38 ASP n 1 39 TYR n 1 40 MET n 1 41 ASN n 1 42 LEU n 1 43 TYR n 1 44 LEU n 1 45 THR n 1 46 ASN n 1 47 ALA n 1 48 MET n 1 49 GLU n 1 50 CYS n 1 51 LYS n 1 52 GLY n 1 53 GLU n 1 54 GLU n 1 55 LYS n 1 56 VAL n 1 57 ARG n 1 58 SER n 1 59 LEU n 1 60 GLY n 1 61 GLU n 1 62 ILE n 1 63 VAL n 1 64 LEU n 1 65 ARG n 1 66 GLY n 1 67 ASN n 1 68 ASN n 1 69 VAL n 1 70 VAL n 1 71 LEU n 1 72 ILE n 1 73 GLN n 1 74 PRO n 1 75 GLN n 1 76 GLU n 1 77 GLU 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 Archaeoglobus _entity_src_gen.pdbx_gene_src_gene AF0362 _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 'Archaeoglobus fulgidus' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 2234 _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 BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _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 'Escherichia coli' _entity_src_gen.pdbx_host_org_tissue ? _entity_src_gen.pdbx_host_org_tissue_fraction ? _entity_src_gen.pdbx_host_org_strain 'BL21(DE3)' _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 'modified pET24d' _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code O29885_ARCFU _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code MVLPNQMVKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKGEEKVRSLGEIVLRGNNVVLIQPQEE _struct_ref.pdbx_align_begin 1 _struct_ref.pdbx_db_accession O29885 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 1LJO _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 1 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 77 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession O29885 _struct_ref_seq.db_align_beg 1 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 75 _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 77 # loop_ _struct_ref_seq_dif.align_id _struct_ref_seq_dif.pdbx_pdb_id_code _struct_ref_seq_dif.mon_id _struct_ref_seq_dif.pdbx_pdb_strand_id _struct_ref_seq_dif.seq_num _struct_ref_seq_dif.pdbx_pdb_ins_code _struct_ref_seq_dif.pdbx_seq_db_name _struct_ref_seq_dif.pdbx_seq_db_accession_code _struct_ref_seq_dif.db_mon_id _struct_ref_seq_dif.pdbx_seq_db_seq_num _struct_ref_seq_dif.details _struct_ref_seq_dif.pdbx_auth_seq_num _struct_ref_seq_dif.pdbx_ordinal 1 1LJO GLY A 1 ? UNP O29885 ? ? 'CLONING ARTIFACT' 1 1 1 1LJO ALA A 2 ? UNP O29885 ? ? 'CLONING ARTIFACT' 2 2 # 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 ACY non-polymer . 'ACETIC ACID' ? 'C2 H4 O2' 60.052 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 CD non-polymer . 'CADMIUM ION' ? 'Cd 2' 112.411 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 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 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.entry_id 1LJO _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 32.92 _exptl_crystal.density_Matthews 1.83 _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp 293 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 3.6 _exptl_crystal_grow.pdbx_details 'ammonium sulphate, lithium sulphate, sodium sulphate, pH 3.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K' _exptl_crystal_grow.pdbx_pH_range . # loop_ _diffrn.id _diffrn.ambient_temp _diffrn.ambient_temp_details _diffrn.crystal_id 1 100 ? 1 2 100 ? 1 1,2 ? ? 1 # loop_ _diffrn_detector.diffrn_id _diffrn_detector.detector _diffrn_detector.type _diffrn_detector.pdbx_collection_date _diffrn_detector.details 1 CCD MARRESEARCH 1999-04-29 ? 2 'IMAGE PLATE' MARRESEARCH 1999-04-20 ? # loop_ _diffrn_radiation.diffrn_id _diffrn_radiation.wavelength_id _diffrn_radiation.pdbx_monochromatic_or_laue_m_l _diffrn_radiation.monochromator _diffrn_radiation.pdbx_diffrn_protocol _diffrn_radiation.pdbx_scattering_type 1 1 M 'Si 111' 'SINGLE WAVELENGTH' x-ray 2 1 M 'Ni MIRROR + Ni FILTER' 'SINGLE WAVELENGTH' x-ray # loop_ _diffrn_radiation_wavelength.id _diffrn_radiation_wavelength.wavelength _diffrn_radiation_wavelength.wt 1 1 1.0 2 1.5418 1.0 # loop_ _diffrn_source.diffrn_id _diffrn_source.source _diffrn_source.type _diffrn_source.pdbx_synchrotron_site _diffrn_source.pdbx_synchrotron_beamline _diffrn_source.pdbx_wavelength _diffrn_source.pdbx_wavelength_list 1 SYNCHROTRON 'ESRF BEAMLINE BM14' ESRF BM14 ? 1 2 'ROTATING ANODE' 'ELLIOTT GX-21' ? ? ? 1.5418 # _reflns.entry_id 1LJO _reflns.observed_criterion_sigma_I 0 _reflns.observed_criterion_sigma_F 0 _reflns.d_resolution_low 27.10 _reflns.d_resolution_high 1.95 _reflns.number_obs 4522 _reflns.number_all 4522 _reflns.percent_possible_obs 97.6 _reflns.pdbx_Rmerge_I_obs 0.0510000 _reflns.pdbx_Rsym_value 0.0510000 _reflns.pdbx_netI_over_sigmaI 10.5 _reflns.B_iso_Wilson_estimate 18.567 _reflns.pdbx_redundancy 2.7 _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_ordinal 1 _reflns.pdbx_diffrn_id 1,2 # _reflns_shell.d_res_high 1.95 _reflns_shell.d_res_low 2.06 _reflns_shell.percent_possible_all 90.9 _reflns_shell.Rmerge_I_obs 0.1730000 _reflns_shell.pdbx_Rsym_value 0.1730000 _reflns_shell.meanI_over_sigI_obs 4.2 _reflns_shell.pdbx_redundancy 2 _reflns_shell.percent_possible_obs ? _reflns_shell.number_unique_all 598 _reflns_shell.pdbx_ordinal 1 _reflns_shell.pdbx_diffrn_id 1,2 # _refine.entry_id 1LJO _refine.ls_number_reflns_obs 4521 _refine.ls_number_reflns_all 4681 _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 0 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_d_res_low 27.10 _refine.ls_d_res_high 1.95 _refine.ls_percent_reflns_obs 96.6 _refine.ls_R_factor_obs 0.1950000 _refine.ls_R_factor_all 0.1950000 _refine.ls_R_factor_R_work 0.1940000 _refine.ls_R_factor_R_free 0.2110000 _refine.ls_R_factor_R_free_error 0.014 _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.0 _refine.ls_number_reflns_R_free 226 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.B_iso_mean 25 _refine.aniso_B[1][1] -5.74 _refine.aniso_B[2][2] -5.74 _refine.aniso_B[3][3] 11.48 _refine.aniso_B[1][2] -1.46 _refine.aniso_B[1][3] 0.00 _refine.aniso_B[2][3] 0.00 _refine.solvent_model_details 'flat model' _refine.solvent_model_param_ksol 0.379594 _refine.solvent_model_param_bsol 56.1311 _refine.pdbx_solvent_vdw_probe_radii ? _refine.pdbx_solvent_ion_probe_radii ? _refine.pdbx_solvent_shrinkage_radii ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'MAXIMUM LIKELIHOOD TARGET' _refine.pdbx_starting_model 'Built by ARP/WARP (68 residues)' _refine.pdbx_method_to_determine_struct SIRAS _refine.pdbx_isotropic_thermal_model ISOTROPIC _refine.pdbx_stereochemistry_target_values 'Engh & Huber' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R_Free ? _refine.overall_SU_B ? _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.overall_SU_ML ? _refine.pdbx_overall_ESU_R ? _refine.pdbx_data_cutoff_high_rms_absF ? _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_analyze.entry_id 1LJO _refine_analyze.Luzzati_coordinate_error_obs 0.20 _refine_analyze.Luzzati_sigma_a_obs 0.11 _refine_analyze.Luzzati_d_res_low_obs 5.00 _refine_analyze.Luzzati_coordinate_error_free 0.24 _refine_analyze.Luzzati_sigma_a_free 0.24 _refine_analyze.Luzzati_d_res_low_free ? _refine_analyze.number_disordered_residues ? _refine_analyze.occupancy_sum_hydrogen ? _refine_analyze.occupancy_sum_non_hydrogen ? _refine_analyze.pdbx_Luzzati_d_res_high_obs ? _refine_analyze.pdbx_refine_id 'X-RAY DIFFRACTION' # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 578 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 13 _refine_hist.number_atoms_solvent 33 _refine_hist.number_atoms_total 624 _refine_hist.d_res_high 1.95 _refine_hist.d_res_low 27.10 # 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 c_bond_d 0.005357 ? ? ? 'X-RAY DIFFRACTION' ? c_angle_deg 1.32164 ? ? ? 'X-RAY DIFFRACTION' ? c_dihedral_angle_d 25.47853 ? ? ? 'X-RAY DIFFRACTION' ? c_improper_angle_d 0.72657 ? ? ? 'X-RAY DIFFRACTION' ? c_mcbond_it 2.255 ? ? ? 'X-RAY DIFFRACTION' ? c_scbond_it 3.077 ? ? ? 'X-RAY DIFFRACTION' ? c_mcangle_it 3.363 ? ? ? 'X-RAY DIFFRACTION' ? c_scangle_it 4.729 ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_total_number_of_bins_used 6 _refine_ls_shell.d_res_high 1.95 _refine_ls_shell.d_res_low 2.07 _refine_ls_shell.number_reflns_R_work 670 _refine_ls_shell.R_factor_R_work 0.1990000 _refine_ls_shell.percent_reflns_obs 91.5 _refine_ls_shell.R_factor_R_free 0.2940000 _refine_ls_shell.R_factor_R_free_error 0.048 _refine_ls_shell.percent_reflns_R_free 5.4 _refine_ls_shell.number_reflns_R_free 38 _refine_ls_shell.number_reflns_obs 708 _refine_ls_shell.redundancy_reflns_obs ? _refine_ls_shell.number_reflns_all ? _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.R_factor_all ? # loop_ _pdbx_xplor_file.serial_no _pdbx_xplor_file.param_file _pdbx_xplor_file.topol_file _pdbx_xplor_file.pdbx_refine_id 1 PROTEIN_REP.PARAM PROTEIN.TOP 'X-RAY DIFFRACTION' 2 WATER_REP.PARAM WATER.TOP 'X-RAY DIFFRACTION' 3 ION.PARAM ION.TOP 'X-RAY DIFFRACTION' 4 ACY.PAR ACY.TOP 'X-RAY DIFFRACTION' # _struct.entry_id 1LJO _struct.title 'CRYSTAL STRUCTURE OF AN SM-LIKE PROTEIN (AF-SM2) FROM ARCHAEOGLOBUS FULGIDUS AT 1.95A RESOLUTION' _struct.pdbx_descriptor 'Archaeal Sm-like protein AF-Sm2' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 1LJO _struct_keywords.pdbx_keywords 'UNKNOWN FUNCTION' _struct_keywords.text 'SNRNP, SM, CORE SNRNP DOMAIN, RNA BINDING PROTEIN, Unknown Function' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? D N N 3 ? E N N 3 ? F N N 4 ? # _struct_biol.id 1 _struct_biol.details ;The biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operations: -Y,X-Y,Z; Y-X,-X,Z; -X,-Y,Z; Y,Y-X,Z and X-Y,X,Z ; _struct_biol.pdbx_parent_biol_id ? # 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 LEU A 5 ? MET A 13 ? LEU A 5 MET A 13 1 ? 9 HELX_P HELX_P2 2 ARG A 65 ? ASN A 67 ? ARG A 65 ASN A 67 5 ? 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_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 ? anti-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 GLU A 54 ? LEU A 64 ? GLU A 54 LEU A 64 A 2 LEU A 42 ? LYS A 51 ? LEU A 42 LYS A 51 A 3 GLN A 28 ? VAL A 36 ? GLN A 28 VAL A 36 A 4 ILE A 17 ? MET A 22 ? ILE A 17 MET A 22 A 5 VAL A 69 ? PRO A 74 ? VAL A 69 PRO A 74 # 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 LEU A 64 ? O LEU A 64 N LEU A 42 ? N LEU A 42 A 2 3 O CYS A 50 ? O CYS A 50 N GLN A 28 ? N GLN A 28 A 3 4 O LEU A 29 ? O LEU A 29 N VAL A 20 ? N VAL A 20 A 4 5 N GLU A 21 ? N GLU A 21 O VAL A 70 ? O VAL A 70 # 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 ? ? ? ? 3 'BINDING SITE FOR RESIDUE ACY A 201' AC2 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE ACY A 202' AC3 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE ACY A 203' # 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 3 GLN A 28 ? GLN A 28 . ? 1_555 ? 2 AC1 3 ASP A 38 ? ASP A 38 . ? 1_554 ? 3 AC1 3 LYS A 51 ? LYS A 51 . ? 1_555 ? 4 AC2 3 LYS A 55 ? LYS A 55 . ? 1_555 ? 5 AC2 3 LYS A 55 ? LYS A 55 . ? 4_565 ? 6 AC2 3 SER A 58 ? SER A 58 . ? 1_555 ? 7 AC3 5 ILE A 17 ? ILE A 17 . ? 4_565 ? 8 AC3 5 ASN A 46 ? ASN A 46 . ? 4_565 ? 9 AC3 5 GLY A 60 ? GLY A 60 . ? 1_555 ? 10 AC3 5 GLU A 61 ? GLU A 61 . ? 1_555 ? 11 AC3 5 HOH F . ? HOH A 385 . ? 1_555 ? # _database_PDB_matrix.entry_id 1LJO _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 1LJO _atom_sites.fract_transf_matrix[1][1] 0.017117 _atom_sites.fract_transf_matrix[1][2] 0.009883 _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] 0.019766 _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] 0.031168 _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 CD N O S # 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 1 1 GLY GLY A . n A 1 2 ALA 2 2 2 ALA ALA A . n A 1 3 MET 3 3 3 MET MET A . n A 1 4 VAL 4 4 4 VAL VAL A . n A 1 5 LEU 5 5 5 LEU LEU A . n A 1 6 PRO 6 6 6 PRO PRO A . n A 1 7 ASN 7 7 7 ASN ASN A . n A 1 8 GLN 8 8 8 GLN GLN A . n A 1 9 MET 9 9 9 MET MET A . n A 1 10 VAL 10 10 10 VAL VAL A . n A 1 11 LYS 11 11 11 LYS LYS A . n A 1 12 SER 12 12 12 SER SER A . n A 1 13 MET 13 13 13 MET MET A . n A 1 14 VAL 14 14 14 VAL VAL A . n A 1 15 GLY 15 15 15 GLY GLY A . n A 1 16 LYS 16 16 16 LYS LYS A . n A 1 17 ILE 17 17 17 ILE ILE A . n A 1 18 ILE 18 18 18 ILE ILE A . n A 1 19 ARG 19 19 19 ARG ARG A . n A 1 20 VAL 20 20 20 VAL VAL A . n A 1 21 GLU 21 21 21 GLU GLU A . n A 1 22 MET 22 22 22 MET MET A . n A 1 23 LYS 23 23 23 LYS LYS A . n A 1 24 GLY 24 24 24 GLY GLY A . n A 1 25 GLU 25 25 25 GLU GLU A . n A 1 26 GLU 26 26 26 GLU GLU A . n A 1 27 ASN 27 27 27 ASN ASN A . n A 1 28 GLN 28 28 28 GLN GLN A . n A 1 29 LEU 29 29 29 LEU LEU A . n A 1 30 VAL 30 30 30 VAL VAL A . n A 1 31 GLY 31 31 31 GLY GLY A . n A 1 32 LYS 32 32 32 LYS LYS A . n A 1 33 LEU 33 33 33 LEU LEU A . n A 1 34 GLU 34 34 34 GLU GLU A . n A 1 35 GLY 35 35 35 GLY GLY A . n A 1 36 VAL 36 36 36 VAL VAL A . n A 1 37 ASP 37 37 37 ASP ASP A . n A 1 38 ASP 38 38 38 ASP ASP A . n A 1 39 TYR 39 39 39 TYR TYR A . n A 1 40 MET 40 40 40 MET MET A . n A 1 41 ASN 41 41 41 ASN ASN A . n A 1 42 LEU 42 42 42 LEU LEU A . n A 1 43 TYR 43 43 43 TYR TYR A . n A 1 44 LEU 44 44 44 LEU LEU A . n A 1 45 THR 45 45 45 THR THR A . n A 1 46 ASN 46 46 46 ASN ASN A . n A 1 47 ALA 47 47 47 ALA ALA A . n A 1 48 MET 48 48 48 MET MET A . n A 1 49 GLU 49 49 49 GLU GLU A . n A 1 50 CYS 50 50 50 CYS CYS A . n A 1 51 LYS 51 51 51 LYS LYS A . n A 1 52 GLY 52 52 52 GLY GLY A . n A 1 53 GLU 53 53 53 GLU GLU A . n A 1 54 GLU 54 54 54 GLU GLU A . n A 1 55 LYS 55 55 55 LYS LYS A . n A 1 56 VAL 56 56 56 VAL VAL A . n A 1 57 ARG 57 57 57 ARG ARG A . n A 1 58 SER 58 58 58 SER SER A . n A 1 59 LEU 59 59 59 LEU LEU A . n A 1 60 GLY 60 60 60 GLY GLY A . n A 1 61 GLU 61 61 61 GLU GLU A . n A 1 62 ILE 62 62 62 ILE ILE A . n A 1 63 VAL 63 63 63 VAL VAL A . n A 1 64 LEU 64 64 64 LEU LEU A . n A 1 65 ARG 65 65 65 ARG ARG A . n A 1 66 GLY 66 66 66 GLY GLY A . n A 1 67 ASN 67 67 67 ASN ASN A . n A 1 68 ASN 68 68 68 ASN ASN A . n A 1 69 VAL 69 69 69 VAL VAL A . n A 1 70 VAL 70 70 70 VAL VAL A . n A 1 71 LEU 71 71 71 LEU LEU A . n A 1 72 ILE 72 72 72 ILE ILE A . n A 1 73 GLN 73 73 73 GLN GLN A . n A 1 74 PRO 74 74 74 PRO PRO A . n A 1 75 GLN 75 75 75 GLN GLN A . n A 1 76 GLU 76 76 ? ? ? A . n A 1 77 GLU 77 77 ? ? ? A . n # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 CD 1 78 76 CD CD A . C 3 ACY 1 201 201 ACY ACY A . D 3 ACY 1 202 202 ACY ACY A . E 3 ACY 1 203 203 ACY ACY A . F 4 HOH 1 307 307 HOH HOH A . F 4 HOH 2 309 309 HOH HOH A . F 4 HOH 3 316 316 HOH HOH A . F 4 HOH 4 317 317 HOH HOH A . F 4 HOH 5 319 319 HOH HOH A . F 4 HOH 6 320 320 HOH HOH A . F 4 HOH 7 323 323 HOH HOH A . F 4 HOH 8 324 324 HOH HOH A . F 4 HOH 9 330 330 HOH HOH A . F 4 HOH 10 377 377 HOH HOH A . F 4 HOH 11 382 382 HOH HOH A . F 4 HOH 12 385 385 HOH HOH A . F 4 HOH 13 387 387 HOH HOH A . F 4 HOH 14 398 398 HOH HOH A . F 4 HOH 15 401 401 HOH HOH A . F 4 HOH 16 404 404 HOH HOH A . F 4 HOH 17 405 405 HOH HOH A . F 4 HOH 18 409 409 HOH HOH A . F 4 HOH 19 411 411 HOH HOH A . F 4 HOH 20 415 415 HOH HOH A . F 4 HOH 21 421 421 HOH HOH A . F 4 HOH 22 422 422 HOH HOH A . F 4 HOH 23 424 424 HOH HOH A . F 4 HOH 24 426 426 HOH HOH A . F 4 HOH 25 428 428 HOH HOH A . F 4 HOH 26 430 430 HOH HOH A . F 4 HOH 27 431 431 HOH HOH A . F 4 HOH 28 436 436 HOH HOH A . F 4 HOH 29 442 442 HOH HOH A . F 4 HOH 30 443 443 HOH HOH A . F 4 HOH 31 444 444 HOH HOH A . F 4 HOH 32 445 445 HOH HOH A . F 4 HOH 33 446 446 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F # 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)' 11110 ? 1 MORE -74 ? 1 'SSA (A^2)' 20190 ? # 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_555 -y,x-y,z -0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 3 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 -0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 4 'crystal symmetry operation' 4_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 5 'crystal symmetry operation' 5_555 y,-x+y,z 0.5000000000 0.8660254038 0.0000000000 0.0000000000 -0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 6 'crystal symmetry operation' 6_555 x-y,x,z 0.5000000000 -0.8660254038 0.0000000000 0.0000000000 0.8660254038 0.5000000000 0.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 # loop_ _pdbx_struct_special_symmetry.id _pdbx_struct_special_symmetry.PDB_model_num _pdbx_struct_special_symmetry.auth_asym_id _pdbx_struct_special_symmetry.auth_comp_id _pdbx_struct_special_symmetry.auth_seq_id _pdbx_struct_special_symmetry.PDB_ins_code _pdbx_struct_special_symmetry.label_asym_id _pdbx_struct_special_symmetry.label_comp_id _pdbx_struct_special_symmetry.label_seq_id 1 1 A CD 78 ? B CD . 2 1 A HOH 307 ? F HOH . 3 1 A HOH 309 ? F HOH . 4 1 A HOH 398 ? F HOH . 5 1 A HOH 442 ? F HOH . 6 1 A HOH 444 ? F HOH . # 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 2002-07-03 2 'Structure model' 1 1 2008-04-28 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2017-10-11 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # loop_ _pdbx_audit_revision_group.ordinal _pdbx_audit_revision_group.revision_ordinal _pdbx_audit_revision_group.data_content_type _pdbx_audit_revision_group.group 1 2 'Structure model' 'Version format compliance' 2 3 'Structure model' 'Derived calculations' 3 3 'Structure model' 'Version format compliance' 4 4 'Structure model' 'Refinement description' # _pdbx_audit_revision_category.ordinal 1 _pdbx_audit_revision_category.revision_ordinal 4 _pdbx_audit_revision_category.data_content_type 'Structure model' _pdbx_audit_revision_category.category software # loop_ _pdbx_audit_revision_item.ordinal _pdbx_audit_revision_item.revision_ordinal _pdbx_audit_revision_item.data_content_type _pdbx_audit_revision_item.item 1 4 'Structure model' '_software.classification' 2 4 'Structure model' '_software.name' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal SHARP phasing . ? 1 CNS refinement . ? 2 MAR345 'data collection' . ? 3 XDS 'data scaling' . ? 4 # _pdbx_database_remark.id 600 _pdbx_database_remark.text ;HETEROGEN Cd ion sitting on six-fold axis is modelling a sulphate ion ; # loop_ _pdbx_unobs_or_zero_occ_residues.id _pdbx_unobs_or_zero_occ_residues.PDB_model_num _pdbx_unobs_or_zero_occ_residues.polymer_flag _pdbx_unobs_or_zero_occ_residues.occupancy_flag _pdbx_unobs_or_zero_occ_residues.auth_asym_id _pdbx_unobs_or_zero_occ_residues.auth_comp_id _pdbx_unobs_or_zero_occ_residues.auth_seq_id _pdbx_unobs_or_zero_occ_residues.PDB_ins_code _pdbx_unobs_or_zero_occ_residues.label_asym_id _pdbx_unobs_or_zero_occ_residues.label_comp_id _pdbx_unobs_or_zero_occ_residues.label_seq_id 1 1 Y 1 A GLU 76 ? A GLU 76 2 1 Y 1 A GLU 77 ? A GLU 77 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'CADMIUM ION' CD 3 'ACETIC ACID' ACY 4 water HOH #