data_3PMT # _entry.id 3PMT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.370 _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 3PMT pdb_00003pmt 10.2210/pdb3pmt/pdb RCSB RCSB062565 ? ? WWPDB D_1000062565 ? ? # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 3S6W _pdbx_database_related.details . _pdbx_database_related.content_type unspecified # _pdbx_database_status.entry_id 3PMT _pdbx_database_status.deposit_site RCSB _pdbx_database_status.process_site RCSB _pdbx_database_status.recvd_initial_deposition_date 2010-11-18 _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf REL _pdbx_database_status.status_code_mr ? _pdbx_database_status.SG_entry 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 'Lam, R.' 1 'Bian, C.B.' 2 'Guo, Y.H.' 3 'Xu, C.' 4 'Kania, J.' 5 'Bountra, C.' 6 'Weigelt, J.' 7 'Arrowsmith, C.H.' 8 'Edwards, A.M.' 9 'Bochkarev, A.' 10 'Min, J.' 11 'Structural Genomics Consortium (SGC)' 12 # _citation.id primary _citation.title 'Crystal Structure of TDRD3 and Methyl-Arginine Binding Characterization of TDRD3, SMN and SPF30.' _citation.journal_abbrev 'Plos One' _citation.journal_volume 7 _citation.page_first e30375 _citation.page_last e30375 _citation.year 2012 _citation.journal_id_ASTM ? _citation.country US _citation.journal_id_ISSN 1932-6203 _citation.journal_id_CSD ? _citation.book_publisher ? _citation.pdbx_database_id_PubMed 22363433 _citation.pdbx_database_id_DOI 10.1371/journal.pone.0030375 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Liu, K.' 1 ? primary 'Guo, Y.' 2 ? primary 'Liu, H.' 3 ? primary 'Bian, C.' 4 ? primary 'Lam, R.' 5 ? primary 'Liu, Y.' 6 ? primary 'Mackenzie, F.' 7 ? primary 'Rojas, L.A.' 8 ? primary 'Reinberg, D.' 9 ? primary 'Bedford, M.T.' 10 ? primary 'Xu, R.M.' 11 ? primary 'Min, J.' 12 ? # _cell.length_a 41.682 _cell.length_b 41.682 _cell.length_c 59.947 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 120.000 _cell.entry_id 3PMT _cell.pdbx_unique_axis ? _cell.Z_PDB 6 _cell.length_a_esd ? _cell.length_b_esd ? _cell.length_c_esd ? _cell.angle_alpha_esd ? _cell.angle_beta_esd ? _cell.angle_gamma_esd ? # _symmetry.space_group_name_H-M 'P 65' _symmetry.entry_id 3PMT _symmetry.Int_Tables_number 170 _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 'Tudor domain-containing protein 3' 6883.764 1 ? ? 'Tudor domain, UNP residues 553-611' ? 2 non-polymer syn 'TETRAETHYLENE GLYCOL' 194.226 1 ? ? ? ? 3 water nat water 18.015 36 ? ? ? ? # _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 AKMWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPIQTE _entity_poly.pdbx_seq_one_letter_code_can AKMWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPIQTE _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 ALA n 1 2 LYS n 1 3 MET n 1 4 TRP n 1 5 LYS n 1 6 PRO n 1 7 GLY n 1 8 ASP n 1 9 GLU n 1 10 CYS n 1 11 PHE n 1 12 ALA n 1 13 LEU n 1 14 TYR n 1 15 TRP n 1 16 GLU n 1 17 ASP n 1 18 ASN n 1 19 LYS n 1 20 PHE n 1 21 TYR n 1 22 ARG n 1 23 ALA n 1 24 GLU n 1 25 VAL n 1 26 GLU n 1 27 ALA n 1 28 LEU n 1 29 HIS n 1 30 SER n 1 31 SER n 1 32 GLY n 1 33 MET n 1 34 THR n 1 35 ALA n 1 36 VAL n 1 37 VAL n 1 38 LYS n 1 39 PHE n 1 40 ILE n 1 41 ASP n 1 42 TYR n 1 43 GLY n 1 44 ASN n 1 45 TYR n 1 46 GLU n 1 47 GLU n 1 48 VAL n 1 49 LEU n 1 50 LEU n 1 51 SER n 1 52 ASN n 1 53 ILE n 1 54 LYS n 1 55 PRO n 1 56 ILE n 1 57 GLN n 1 58 THR n 1 59 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 human _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene TDRD3 _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 'Homo sapiens' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 9606 _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 469008 _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)-V2R-pRARE2' _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 pET28-MHL _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code TDRD3_HUMAN _struct_ref.pdbx_db_accession Q9H7E2 _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code AKMWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFIDYGNYEEVLLSNIKPIQTE _struct_ref.pdbx_align_begin 553 _struct_ref.pdbx_db_isoform ? # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 3PMT _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 59 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession Q9H7E2 _struct_ref_seq.db_align_beg 553 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 611 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 553 _struct_ref_seq.pdbx_auth_seq_align_end 611 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158 GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162 HOH non-polymer . WATER ? 'H2 O' 18.015 ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173 LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211 PG4 non-polymer . 'TETRAETHYLENE GLYCOL' ? 'C8 H18 O5' 194.226 PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189 PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130 SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093 THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119 TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225 TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189 VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146 # _exptl.crystals_number 1 _exptl.entry_id 3PMT _exptl.method 'X-RAY DIFFRACTION' # _exptl_crystal.id 1 _exptl_crystal.density_Matthews 2.18 _exptl_crystal.density_meas ? _exptl_crystal.density_percent_sol 43.68 _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 8.5 _exptl_crystal_grow.temp 291 _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pdbx_details '0.1M Tris-HCl pH 8.5, 2.0M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 291K' _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 'RIGAKU SATURN A200' _diffrn_detector.pdbx_collection_date 2010-01-12 _diffrn_detector.details 'VariMax HF' # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.monochromator graphite _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5418 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source 'ROTATING ANODE' _diffrn_source.type 'RIGAKU FR-E SUPERBRIGHT' _diffrn_source.pdbx_wavelength ? _diffrn_source.pdbx_wavelength_list 1.5418 _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id 3PMT _reflns.d_resolution_high 1.800 _reflns.d_resolution_low 50.000 _reflns.number_obs 5478 _reflns.pdbx_Rmerge_I_obs 0.031 _reflns.pdbx_netI_over_sigmaI 35.400 _reflns.pdbx_chi_squared 1.108 _reflns.pdbx_redundancy 19.500 _reflns.percent_possible_obs 98.700 _reflns.observed_criterion_sigma_F ? _reflns.observed_criterion_sigma_I ? _reflns.number_all ? _reflns.pdbx_Rsym_value ? _reflns.B_iso_Wilson_estimate ? _reflns.R_free_details ? _reflns.limit_h_max ? _reflns.limit_h_min ? _reflns.limit_k_max ? _reflns.limit_k_min ? _reflns.limit_l_max ? _reflns.limit_l_min ? _reflns.observed_criterion_F_max ? _reflns.observed_criterion_F_min ? _reflns.pdbx_scaling_rejects ? _reflns.pdbx_ordinal 1 _reflns.pdbx_diffrn_id 1 # loop_ _reflns_shell.d_res_high _reflns_shell.d_res_low _reflns_shell.number_measured_obs _reflns_shell.number_measured_all _reflns_shell.number_unique_obs _reflns_shell.Rmerge_I_obs _reflns_shell.meanI_over_sigI_obs _reflns_shell.pdbx_Rsym_value _reflns_shell.pdbx_chi_squared _reflns_shell.pdbx_redundancy _reflns_shell.percent_possible_obs _reflns_shell.number_unique_all _reflns_shell.percent_possible_all _reflns_shell.pdbx_ordinal _reflns_shell.pdbx_diffrn_id 1.800 1.840 ? ? ? 0.099 ? ? 0.913 8.500 ? 314 85.800 1 1 1.840 1.890 ? ? ? 0.098 ? ? 0.833 11.600 ? 358 97.500 2 1 1.890 1.940 ? ? ? 0.089 ? ? 1.036 15.700 ? 353 97.500 3 1 1.940 2.000 ? ? ? 0.078 ? ? 1.108 18.200 ? 377 100.000 4 1 2.000 2.060 ? ? ? 0.072 ? ? 1.116 20.100 ? 362 100.000 5 1 2.060 2.130 ? ? ? 0.064 ? ? 1.180 20.800 ? 368 100.000 6 1 2.130 2.220 ? ? ? 0.055 ? ? 1.139 21.400 ? 369 100.000 7 1 2.220 2.320 ? ? ? 0.054 ? ? 1.125 21.600 ? 370 100.000 8 1 2.320 2.440 ? ? ? 0.046 ? ? 1.109 21.800 ? 370 100.000 9 1 2.440 2.600 ? ? ? 0.042 ? ? 1.156 21.900 ? 369 100.000 10 1 2.600 2.800 ? ? ? 0.036 ? ? 1.139 21.900 ? 366 100.000 11 1 2.800 3.080 ? ? ? 0.030 ? ? 1.099 22.000 ? 366 100.000 12 1 3.080 3.520 ? ? ? 0.025 ? ? 1.121 22.100 ? 373 100.000 13 1 3.520 4.440 ? ? ? 0.022 ? ? 1.049 22.000 ? 377 100.000 14 1 4.440 50.000 ? ? ? 0.021 ? ? 1.209 21.000 ? 386 99.000 15 1 # _refine.entry_id 3PMT _refine.ls_d_res_high 1.8000 _refine.ls_d_res_low 19.6900 _refine.pdbx_ls_sigma_F 0.000 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.ls_percent_reflns_obs 98.8200 _refine.ls_number_reflns_obs 5444 _refine.ls_number_reflns_all ? _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.pdbx_R_Free_selection_details RANDOM _refine.details 'HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED' _refine.ls_R_factor_all ? _refine.ls_R_factor_obs 0.1789 _refine.ls_R_factor_R_work 0.1775 _refine.ls_wR_factor_R_work 0.1790 _refine.ls_R_factor_R_free 0.2089 _refine.ls_wR_factor_R_free 0.2250 _refine.ls_percent_reflns_R_free 4.5000 _refine.ls_number_reflns_R_free 247 _refine.ls_R_factor_R_free_error ? _refine.B_iso_mean 26.4207 _refine.solvent_model_param_bsol ? _refine.solvent_model_param_ksol ? _refine.pdbx_isotropic_thermal_model ? _refine.aniso_B[1][1] -0.1300 _refine.aniso_B[2][2] -0.1300 _refine.aniso_B[3][3] 0.1900 _refine.aniso_B[1][2] -0.0600 _refine.aniso_B[1][3] 0.0000 _refine.aniso_B[2][3] 0.0000 _refine.correlation_coeff_Fo_to_Fc 0.9560 _refine.correlation_coeff_Fo_to_Fc_free 0.9380 _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.pdbx_overall_ESU_R_Free 0.1190 _refine.overall_SU_ML 0.0830 _refine.overall_SU_B 5.2030 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.pdbx_solvent_vdw_probe_radii 1.2000 _refine.pdbx_solvent_ion_probe_radii 0.8000 _refine.pdbx_solvent_shrinkage_radii 0.8000 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.overall_FOM_work_R_set ? _refine.B_iso_max 68.820 _refine.B_iso_min 14.570 _refine.occupancy_max 1.000 _refine.occupancy_min 0.500 _refine.pdbx_ls_sigma_I ? _refine.ls_redundancy_reflns_obs ? _refine.ls_R_factor_R_free_error_details ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.overall_FOM_free_R_set ? _refine.pdbx_overall_phase_error ? _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.pdbx_overall_ESU_R ? _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.pdbx_overall_SU_R_free_Cruickshank_DPI ? _refine.pdbx_overall_SU_R_Blow_DPI ? _refine.pdbx_overall_SU_R_free_Blow_DPI ? # _refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 447 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 10 _refine_hist.number_atoms_solvent 36 _refine_hist.number_atoms_total 493 _refine_hist.d_res_high 1.8000 _refine_hist.d_res_low 19.6900 # 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 474 0.010 0.022 ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 641 1.161 1.950 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 56 7.258 5.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 23 32.835 24.783 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 74 12.472 15.000 ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 1 30.373 15.000 ? 'X-RAY DIFFRACTION' ? r_chiral_restr 66 0.084 0.200 ? 'X-RAY DIFFRACTION' ? r_gen_planes_refined 360 0.004 0.021 ? 'X-RAY DIFFRACTION' ? # loop_ _refine_ls_shell.pdbx_total_number_of_bins_used _refine_ls_shell.d_res_low _refine_ls_shell.d_res_high _refine_ls_shell.number_reflns_all _refine_ls_shell.percent_reflns_obs _refine_ls_shell.number_reflns_R_work _refine_ls_shell.R_factor_R_work _refine_ls_shell.number_reflns_R_free _refine_ls_shell.R_factor_R_free _refine_ls_shell.number_reflns_obs _refine_ls_shell.R_factor_R_free_error _refine_ls_shell.percent_reflns_R_free _refine_ls_shell.redundancy_reflns_obs _refine_ls_shell.R_factor_all _refine_ls_shell.pdbx_refine_id 20 1.847 1.800 394 87.817 325 0.188 21 0.242 . . . . . 'X-RAY DIFFRACTION' 20 1.897 1.847 400 96.250 369 0.194 16 0.190 . . . . . 'X-RAY DIFFRACTION' 20 1.951 1.897 374 99.733 358 0.173 15 0.214 . . . . . 'X-RAY DIFFRACTION' 20 2.011 1.951 374 100.000 363 0.159 11 0.254 . . . . . 'X-RAY DIFFRACTION' 20 2.076 2.011 365 100.000 347 0.185 18 0.289 . . . . . 'X-RAY DIFFRACTION' 20 2.148 2.076 340 100.000 325 0.185 15 0.206 . . . . . 'X-RAY DIFFRACTION' 20 2.228 2.148 338 100.000 316 0.178 22 0.206 . . . . . 'X-RAY DIFFRACTION' 20 2.318 2.228 327 100.000 317 0.194 10 0.177 . . . . . 'X-RAY DIFFRACTION' 20 2.419 2.318 311 100.000 298 0.192 13 0.225 . . . . . 'X-RAY DIFFRACTION' 20 2.536 2.419 290 100.000 274 0.194 16 0.270 . . . . . 'X-RAY DIFFRACTION' 20 2.670 2.536 292 100.000 274 0.192 18 0.221 . . . . . 'X-RAY DIFFRACTION' 20 2.829 2.670 267 100.000 255 0.186 12 0.198 . . . . . 'X-RAY DIFFRACTION' 20 3.020 2.829 257 100.000 245 0.193 12 0.260 . . . . . 'X-RAY DIFFRACTION' 20 3.256 3.020 234 100.000 226 0.196 8 0.240 . . . . . 'X-RAY DIFFRACTION' 20 3.557 3.256 217 100.000 208 0.166 9 0.243 . . . . . 'X-RAY DIFFRACTION' 20 3.960 3.557 199 100.000 189 0.149 10 0.126 . . . . . 'X-RAY DIFFRACTION' 20 4.542 3.960 179 100.000 175 0.136 4 0.076 . . . . . 'X-RAY DIFFRACTION' 20 5.491 4.542 152 100.000 146 0.150 6 0.118 . . . . . 'X-RAY DIFFRACTION' 20 7.479 5.491 120 100.000 114 0.228 6 0.205 . . . . . 'X-RAY DIFFRACTION' 20 19.685 7.479 79 98.734 73 0.205 5 0.439 . . . . . 'X-RAY DIFFRACTION' # _struct.entry_id 3PMT _struct.title 'Crystal structure of the Tudor domain of human Tudor domain-containing protein 3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag N _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 3PMT _struct_keywords.pdbx_keywords TRANSCRIPTION _struct_keywords.text 'Tudor domain, Structural Genomics Consortium, SGC, sulfur phasing, Nucleus, TRANSCRIPTION' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 3 ? # _struct_biol.id 1 _struct_biol.details ? # _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 TYR A 45 ? LEU A 49 ? TYR A 597 LEU A 601 A 2 THR A 34 ? PHE A 39 ? THR A 586 PHE A 591 A 3 LYS A 19 ? LEU A 28 ? LYS A 571 LEU A 580 A 4 GLU A 9 ? TYR A 14 ? GLU A 561 TYR A 566 A 5 ILE A 53 ? PRO A 55 ? ILE A 605 PRO A 607 # 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 VAL A 48 ? O VAL A 600 N ALA A 35 ? N ALA A 587 A 2 3 O VAL A 36 ? O VAL A 588 N GLU A 26 ? N GLU A 578 A 3 4 O LYS A 19 ? O LYS A 571 N TYR A 14 ? N TYR A 566 A 4 5 N PHE A 11 ? N PHE A 563 O LYS A 54 ? O LYS A 606 # _struct_site.id AC1 _struct_site.pdbx_evidence_code Software _struct_site.pdbx_auth_asym_id A _struct_site.pdbx_auth_comp_id PG4 _struct_site.pdbx_auth_seq_id 800 _struct_site.pdbx_auth_ins_code ? _struct_site.pdbx_num_residues 5 _struct_site.details 'BINDING SITE FOR RESIDUE PG4 A 800' # 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 5 TYR A 14 ? TYR A 566 . ? 1_555 ? 2 AC1 5 LYS A 19 ? LYS A 571 . ? 5_555 ? 3 AC1 5 PHE A 39 ? PHE A 591 . ? 1_555 ? 4 AC1 5 TYR A 42 ? TYR A 594 . ? 1_555 ? 5 AC1 5 ASN A 44 ? ASN A 596 . ? 1_555 ? # _atom_sites.entry_id 3PMT _atom_sites.fract_transf_matrix[1][1] 0.023991 _atom_sites.fract_transf_matrix[1][2] 0.013851 _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] 0.027703 _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] 0.016681 _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 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 ALA 1 553 ? ? ? A . n A 1 2 LYS 2 554 554 LYS LYS A . n A 1 3 MET 3 555 555 MET MET A . n A 1 4 TRP 4 556 556 TRP TRP A . n A 1 5 LYS 5 557 557 LYS LYS A . n A 1 6 PRO 6 558 558 PRO PRO A . n A 1 7 GLY 7 559 559 GLY GLY A . n A 1 8 ASP 8 560 560 ASP ASP A . n A 1 9 GLU 9 561 561 GLU GLU A . n A 1 10 CYS 10 562 562 CYS CYS A . n A 1 11 PHE 11 563 563 PHE PHE A . n A 1 12 ALA 12 564 564 ALA ALA A . n A 1 13 LEU 13 565 565 LEU LEU A . n A 1 14 TYR 14 566 566 TYR TYR A . n A 1 15 TRP 15 567 567 TRP TRP A . n A 1 16 GLU 16 568 568 GLU GLU A . n A 1 17 ASP 17 569 569 ASP ASP A . n A 1 18 ASN 18 570 570 ASN ASN A . n A 1 19 LYS 19 571 571 LYS LYS A . n A 1 20 PHE 20 572 572 PHE PHE A . n A 1 21 TYR 21 573 573 TYR TYR A . n A 1 22 ARG 22 574 574 ARG ARG A . n A 1 23 ALA 23 575 575 ALA ALA A . n A 1 24 GLU 24 576 576 GLU GLU A . n A 1 25 VAL 25 577 577 VAL VAL A . n A 1 26 GLU 26 578 578 GLU GLU A . n A 1 27 ALA 27 579 579 ALA ALA A . n A 1 28 LEU 28 580 580 LEU LEU A . n A 1 29 HIS 29 581 581 HIS HIS A . n A 1 30 SER 30 582 582 SER SER A . n A 1 31 SER 31 583 583 SER SER A . n A 1 32 GLY 32 584 584 GLY GLY A . n A 1 33 MET 33 585 585 MET MET A . n A 1 34 THR 34 586 586 THR THR A . n A 1 35 ALA 35 587 587 ALA ALA A . n A 1 36 VAL 36 588 588 VAL VAL A . n A 1 37 VAL 37 589 589 VAL VAL A . n A 1 38 LYS 38 590 590 LYS LYS A . n A 1 39 PHE 39 591 591 PHE PHE A . n A 1 40 ILE 40 592 592 ILE ILE A . n A 1 41 ASP 41 593 593 ASP ASP A . n A 1 42 TYR 42 594 594 TYR TYR A . n A 1 43 GLY 43 595 595 GLY GLY A . n A 1 44 ASN 44 596 596 ASN ASN A . n A 1 45 TYR 45 597 597 TYR TYR A . n A 1 46 GLU 46 598 598 GLU GLU A . n A 1 47 GLU 47 599 599 GLU GLU A . n A 1 48 VAL 48 600 600 VAL VAL A . n A 1 49 LEU 49 601 601 LEU LEU A . n A 1 50 LEU 50 602 602 LEU LEU A . n A 1 51 SER 51 603 603 SER SER A . n A 1 52 ASN 52 604 604 ASN ASN A . n A 1 53 ILE 53 605 605 ILE ILE A . n A 1 54 LYS 54 606 606 LYS LYS A . n A 1 55 PRO 55 607 607 PRO PRO A . n A 1 56 ILE 56 608 608 ILE ILE A . n A 1 57 GLN 57 609 ? ? ? A . n A 1 58 THR 58 610 ? ? ? A . n A 1 59 GLU 59 611 ? ? ? A . n # _pdbx_SG_project.id 1 _pdbx_SG_project.project_name ? _pdbx_SG_project.full_name_of_center 'Structural Genomics Consortium' _pdbx_SG_project.initial_of_center SGC # 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 PG4 1 800 800 PG4 PG4 A . C 3 HOH 1 1 1 HOH HOH A . C 3 HOH 2 2 2 HOH HOH A . C 3 HOH 3 3 3 HOH HOH A . C 3 HOH 4 4 4 HOH HOH A . C 3 HOH 5 5 5 HOH HOH A . C 3 HOH 6 6 6 HOH HOH A . C 3 HOH 7 7 7 HOH HOH A . C 3 HOH 8 8 8 HOH HOH A . C 3 HOH 9 9 9 HOH HOH A . C 3 HOH 10 10 10 HOH HOH A . C 3 HOH 11 11 11 HOH HOH A . C 3 HOH 12 12 12 HOH HOH A . C 3 HOH 13 13 13 HOH HOH A . C 3 HOH 14 14 14 HOH HOH A . C 3 HOH 15 15 15 HOH HOH A . C 3 HOH 16 16 16 HOH HOH A . C 3 HOH 17 17 17 HOH HOH A . C 3 HOH 18 18 18 HOH HOH A . C 3 HOH 19 19 19 HOH HOH A . C 3 HOH 20 20 20 HOH HOH A . C 3 HOH 21 21 21 HOH HOH A . C 3 HOH 22 22 22 HOH HOH A . C 3 HOH 23 23 23 HOH HOH A . C 3 HOH 24 24 24 HOH HOH A . C 3 HOH 25 25 25 HOH HOH A . C 3 HOH 26 26 26 HOH HOH A . C 3 HOH 27 27 27 HOH HOH A . C 3 HOH 28 28 28 HOH HOH A . C 3 HOH 29 29 29 HOH HOH A . C 3 HOH 30 30 30 HOH HOH A . C 3 HOH 31 31 31 HOH HOH A . C 3 HOH 32 32 32 HOH HOH A . C 3 HOH 33 33 33 HOH HOH A . C 3 HOH 34 34 34 HOH HOH A . C 3 HOH 35 35 35 HOH HOH A . C 3 HOH 36 36 36 HOH HOH A . # _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 # _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 2010-12-01 2 'Structure model' 1 1 2011-07-13 3 'Structure model' 1 2 2012-03-07 4 'Structure model' 1 3 2012-03-28 5 'Structure model' 1 4 2017-11-08 6 'Structure model' 1 5 2023-05-31 # _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' 'Database references' 3 4 'Structure model' 'Database references' 4 5 'Structure model' 'Refinement description' 5 6 'Structure model' 'Database references' 6 6 '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 5 'Structure model' software 2 6 'Structure model' database_2 3 6 '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 6 'Structure model' '_database_2.pdbx_DOI' 2 6 'Structure model' '_database_2.pdbx_database_accession' 3 6 'Structure model' '_struct_site.pdbx_auth_asym_id' 4 6 'Structure model' '_struct_site.pdbx_auth_comp_id' 5 6 'Structure model' '_struct_site.pdbx_auth_seq_id' # _pdbx_refine_tls.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls.id 1 _pdbx_refine_tls.details ? _pdbx_refine_tls.method refined _pdbx_refine_tls.origin_x 14.6410 _pdbx_refine_tls.origin_y 11.0040 _pdbx_refine_tls.origin_z 4.0520 _pdbx_refine_tls.T[1][1] 0.0219 _pdbx_refine_tls.T[2][2] 0.0259 _pdbx_refine_tls.T[3][3] 0.0096 _pdbx_refine_tls.T[1][2] 0.0080 _pdbx_refine_tls.T[1][3] 0.0062 _pdbx_refine_tls.T[2][3] -0.0034 _pdbx_refine_tls.L[1][1] 1.0777 _pdbx_refine_tls.L[2][2] 2.5698 _pdbx_refine_tls.L[3][3] 2.4387 _pdbx_refine_tls.L[1][2] -0.1404 _pdbx_refine_tls.L[1][3] 1.3221 _pdbx_refine_tls.L[2][3] -0.2574 _pdbx_refine_tls.S[1][1] -0.0508 _pdbx_refine_tls.S[2][2] 0.0332 _pdbx_refine_tls.S[3][3] 0.0176 _pdbx_refine_tls.S[1][2] 0.0001 _pdbx_refine_tls.S[1][3] -0.0208 _pdbx_refine_tls.S[2][3] -0.0400 _pdbx_refine_tls.S[2][1] -0.0480 _pdbx_refine_tls.S[3][1] -0.1117 _pdbx_refine_tls.S[3][2] 0.0122 # _pdbx_refine_tls_group.pdbx_refine_id 'X-RAY DIFFRACTION' _pdbx_refine_tls_group.id 1 _pdbx_refine_tls_group.refine_tls_id 1 _pdbx_refine_tls_group.beg_auth_asym_id A _pdbx_refine_tls_group.beg_auth_seq_id 554 _pdbx_refine_tls_group.end_auth_asym_id A _pdbx_refine_tls_group.end_auth_seq_id 608 _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 ? # loop_ _pdbx_phasing_MAD_set.id _pdbx_phasing_MAD_set.d_res_low _pdbx_phasing_MAD_set.d_res_high _pdbx_phasing_MAD_set.reflns_acentric _pdbx_phasing_MAD_set.reflns_centric _pdbx_phasing_MAD_set.power_acentric _pdbx_phasing_MAD_set.power_centric ISO_1 19.69 1.80 5214 232 0.000 0.000 ANO_1 19.69 1.80 5179 0 0.749 0.000 # loop_ _pdbx_phasing_MAD_set_shell.id _pdbx_phasing_MAD_set_shell.d_res_low _pdbx_phasing_MAD_set_shell.d_res_high _pdbx_phasing_MAD_set_shell.reflns_acentric _pdbx_phasing_MAD_set_shell.reflns_centric _pdbx_phasing_MAD_set_shell.power_acentric _pdbx_phasing_MAD_set_shell.power_centric ISO_1 19.69 6.79 88 16 0.000 0.000 ISO_1 6.79 4.95 153 15 0.000 0.000 ISO_1 4.95 4.08 191 14 0.000 0.000 ISO_1 4.08 3.56 235 16 0.000 0.000 ISO_1 3.56 3.19 257 14 0.000 0.000 ISO_1 3.19 2.92 294 16 0.000 0.000 ISO_1 2.92 2.71 312 15 0.000 0.000 ISO_1 2.71 2.54 343 16 0.000 0.000 ISO_1 2.54 2.39 352 13 0.000 0.000 ISO_1 2.39 2.27 381 17 0.000 0.000 ISO_1 2.27 2.17 405 15 0.000 0.000 ISO_1 2.17 2.08 413 14 0.000 0.000 ISO_1 2.08 2.00 441 15 0.000 0.000 ISO_1 2.00 1.92 450 16 0.000 0.000 ISO_1 1.92 1.86 466 10 0.000 0.000 ISO_1 1.86 1.80 433 10 0.000 0.000 ANO_1 19.69 6.79 88 0 1.621 0.000 ANO_1 6.79 4.95 153 0 1.576 0.000 ANO_1 4.95 4.08 191 0 1.037 0.000 ANO_1 4.08 3.56 235 0 1.005 0.000 ANO_1 3.56 3.19 257 0 0.978 0.000 ANO_1 3.19 2.92 294 0 0.995 0.000 ANO_1 2.92 2.71 312 0 0.921 0.000 ANO_1 2.71 2.54 343 0 0.972 0.000 ANO_1 2.54 2.39 352 0 0.863 0.000 ANO_1 2.39 2.27 381 0 0.784 0.000 ANO_1 2.27 2.17 405 0 0.648 0.000 ANO_1 2.17 2.08 413 0 0.550 0.000 ANO_1 2.08 2.00 441 0 0.494 0.000 ANO_1 2.00 1.92 448 0 0.365 0.000 ANO_1 1.92 1.86 460 0 0.289 0.000 ANO_1 1.86 1.80 406 0 0.193 0.000 # _pdbx_phasing_MAD_set_site.id 1 _pdbx_phasing_MAD_set_site.atom_type_symbol S _pdbx_phasing_MAD_set_site.Cartn_x 13.529 _pdbx_phasing_MAD_set_site.Cartn_y 14.745 _pdbx_phasing_MAD_set_site.Cartn_z 10.011 _pdbx_phasing_MAD_set_site.occupancy 1.63 _pdbx_phasing_MAD_set_site.b_iso 24.53 # loop_ _pdbx_phasing_MAD_shell.d_res_low _pdbx_phasing_MAD_shell.d_res_high _pdbx_phasing_MAD_shell.reflns_acentric _pdbx_phasing_MAD_shell.fom_acentric _pdbx_phasing_MAD_shell.reflns_centric _pdbx_phasing_MAD_shell.fom_centric 19.69 6.79 88 0.517 16 0.132 6.79 4.95 153 0.453 15 0.071 4.95 4.08 191 0.392 14 0.078 4.08 3.56 235 0.354 16 0.056 3.56 3.19 257 0.377 14 0.078 3.19 2.92 294 0.368 16 0.087 2.92 2.71 312 0.341 15 0.095 2.71 2.54 343 0.300 16 0.087 2.54 2.39 352 0.265 13 0.074 2.39 2.27 381 0.245 17 0.054 2.27 2.17 405 0.201 15 0.089 2.17 2.08 413 0.192 14 0.040 2.08 2.00 441 0.174 15 0.046 2.00 1.92 450 0.152 16 0.060 1.92 1.86 466 0.121 10 0.048 1.86 1.80 433 0.117 10 0.046 # _pdbx_phasing_dm.entry_id 3PMT _pdbx_phasing_dm.method 'Solvent flattening and Histogram matching' _pdbx_phasing_dm.reflns 5446 # loop_ _pdbx_phasing_dm_shell.d_res_high _pdbx_phasing_dm_shell.d_res_low _pdbx_phasing_dm_shell.delta_phi_final _pdbx_phasing_dm_shell.delta_phi_initial _pdbx_phasing_dm_shell.fom_acentric _pdbx_phasing_dm_shell.fom_centric _pdbx_phasing_dm_shell.fom _pdbx_phasing_dm_shell.reflns_acentric _pdbx_phasing_dm_shell.reflns_centric _pdbx_phasing_dm_shell.reflns 4.020 100.000 69.400 ? ? ? 0.899 ? ? 506 3.180 4.020 71.800 ? ? ? 0.940 ? ? 503 2.780 3.180 70.500 ? ? ? 0.920 ? ? 503 2.520 2.780 68.300 ? ? ? 0.911 ? ? 504 2.340 2.520 66.700 ? ? ? 0.922 ? ? 505 2.200 2.340 70.200 ? ? ? 0.926 ? ? 508 2.090 2.200 82.100 ? ? ? 0.922 ? ? 501 2.000 2.090 79.500 ? ? ? 0.919 ? ? 502 1.920 2.000 79.900 ? ? ? 0.916 ? ? 502 1.800 1.920 83.100 ? ? ? 0.843 ? ? 912 # _phasing.method SAD # _phasing_MAD.entry_id 3PMT _phasing_MAD.pdbx_d_res_low 19.690 _phasing_MAD.pdbx_d_res_high 1.800 _phasing_MAD.pdbx_reflns_acentric 5214 _phasing_MAD.pdbx_fom_acentric 0.247 _phasing_MAD.pdbx_reflns_centric 232 _phasing_MAD.pdbx_fom_centric 0.073 # loop_ _software.pdbx_ordinal _software.name _software.version _software.date _software.type _software.contact_author _software.contact_author_email _software.classification _software.location _software.language _software.citation_id 1 DENZO . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data reduction' http://www.hkl-xray.com/ ? ? 2 SCALEPACK . ? package 'Zbyszek Otwinowski' hkl@hkl-xray.com 'data scaling' http://www.hkl-xray.com/ ? ? 3 SHARP . ? package 'Eric de La Fortelle' sharp-develop@globalphasing.com phasing http://www.globalphasing.com/sharp/ ? ? 4 DM 6.1 ? program 'Kevin Cowtan' kowtan@ysbl.york.ac.uk phasing http://www.ccp4.ac.uk/dist/html/dm.html Fortran_77 ? 5 REFMAC refmac_5.6.0081 24/04/2001 program 'Garib N. Murshudov' garib@ysbl.york.ac.uk refinement http://www.ccp4.ac.uk/dist/html/refmac5.html Fortran_77 ? 6 PDB_EXTRACT 3.10 'June 10, 2010' package PDB deposit@deposit.rcsb.org 'data extraction' http://sw-tools.pdb.org/apps/PDB_EXTRACT/ C++ ? 7 JDirector . ? ? ? ? 'data collection' ? ? ? 8 HKL-2000 . ? ? ? ? 'data reduction' ? ? ? 9 HKL-2000 . ? ? ? ? 'data scaling' ? ? ? # 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 554 ? CG ? A LYS 2 CG 2 1 Y 1 A LYS 554 ? CD ? A LYS 2 CD 3 1 Y 1 A LYS 554 ? CE ? A LYS 2 CE 4 1 Y 1 A LYS 554 ? NZ ? A LYS 2 NZ 5 1 Y 1 A MET 555 ? CG ? A MET 3 CG 6 1 Y 1 A MET 555 ? SD ? A MET 3 SD 7 1 Y 1 A MET 555 ? CE ? A MET 3 CE 8 1 N 1 A PG4 800 ? O1 ? B PG4 1 O1 9 1 N 1 A PG4 800 ? C1 ? B PG4 1 C1 10 1 N 1 A PG4 800 ? C2 ? B PG4 1 C2 # 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 ALA 553 ? A ALA 1 2 1 Y 1 A GLN 609 ? A GLN 57 3 1 Y 1 A THR 610 ? A THR 58 4 1 Y 1 A GLU 611 ? A GLU 59 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 2 'TETRAETHYLENE GLYCOL' PG4 3 water HOH #