data_2VC8 # _entry.id 2VC8 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.279 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2VC8 PDBE EBI-33854 WWPDB D_1290033854 # _pdbx_database_related.db_name PDB _pdbx_database_related.db_id 2RM4 _pdbx_database_related.content_type unspecified _pdbx_database_related.details 'NMR STRUCTURE OF THE LSM DOMAIN OF DROSOPHILA EDC3' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2VC8 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2007-09-19 _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_sf ? _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 'Tritschler, F.' 1 'Hartmann, M.D.' 2 'Weichenrieder, O.' 3 # _citation.id primary _citation.title 'A Divergent Sm Fold in Edc3 Proteins Mediates Dcp1 Binding and P-Body Targeting.' _citation.journal_abbrev Mol.Cell.Biol. _citation.journal_volume 27 _citation.page_first 8600 _citation.page_last ? _citation.year 2007 _citation.journal_id_ASTM MCEBD4 _citation.country US _citation.journal_id_ISSN 0270-7306 _citation.journal_id_CSD 2044 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 17923697 _citation.pdbx_database_id_DOI 10.1128/MCB.01506-07 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal primary 'Tritschler, F.' 1 primary 'Eulalio, A.' 2 primary 'Truffault, V.' 3 primary 'Hartmann, M.D.' 4 primary 'Helms, S.' 5 primary 'Schmidt, S.' 6 primary 'Coles, M.' 7 primary 'Izaurralde, E.' 8 primary 'Weichenrieder, O.' 9 # _cell.entry_id 2VC8 _cell.length_a 37.300 _cell.length_b 37.300 _cell.length_c 79.209 _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 2VC8 _symmetry.space_group_name_H-M 'P 32 2 1' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 # 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 'ENHANCER OF MRNA-DECAPPING PROTEIN 3' 8988.077 1 ? ? 'LSM DOMAIN, RESIDUES 1-82' ? 2 water nat water 18.015 54 ? ? ? ? # _entity_name_com.entity_id 1 _entity_name_com.name 'YJEF DOMAIN-CONTAINING PROTEIN 1, LSM16 HOMOLOG, HUMAN EDC3, EDC3' # _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 ;GAMATDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPGDNQHFGD LHQT ; _entity_poly.pdbx_seq_one_letter_code_can ;GAMATDWLGSIVSINCGDSLGVYQGRVSAVDQVSQTISLTRPFHNGVKCLVPEVTFRAGDITELKILEIPGPGDNQHFGD LHQT ; _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 ALA n 1 5 THR n 1 6 ASP n 1 7 TRP n 1 8 LEU n 1 9 GLY n 1 10 SER n 1 11 ILE n 1 12 VAL n 1 13 SER n 1 14 ILE n 1 15 ASN n 1 16 CYS n 1 17 GLY n 1 18 ASP n 1 19 SER n 1 20 LEU n 1 21 GLY n 1 22 VAL n 1 23 TYR n 1 24 GLN n 1 25 GLY n 1 26 ARG n 1 27 VAL n 1 28 SER n 1 29 ALA n 1 30 VAL n 1 31 ASP n 1 32 GLN n 1 33 VAL n 1 34 SER n 1 35 GLN n 1 36 THR n 1 37 ILE n 1 38 SER n 1 39 LEU n 1 40 THR n 1 41 ARG n 1 42 PRO n 1 43 PHE n 1 44 HIS n 1 45 ASN n 1 46 GLY n 1 47 VAL n 1 48 LYS n 1 49 CYS n 1 50 LEU n 1 51 VAL n 1 52 PRO n 1 53 GLU n 1 54 VAL n 1 55 THR n 1 56 PHE n 1 57 ARG n 1 58 ALA n 1 59 GLY n 1 60 ASP n 1 61 ILE n 1 62 THR n 1 63 GLU n 1 64 LEU n 1 65 LYS n 1 66 ILE n 1 67 LEU n 1 68 GLU n 1 69 ILE n 1 70 PRO n 1 71 GLY n 1 72 PRO n 1 73 GLY n 1 74 ASP n 1 75 ASN n 1 76 GLN n 1 77 HIS n 1 78 PHE n 1 79 GLY n 1 80 ASP n 1 81 LEU n 1 82 HIS n 1 83 GLN n 1 84 THR 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 ? _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) ROSETTA II' _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 ? _entity_src_gen.pdbx_host_org_vector ? _entity_src_gen.host_org_details ? _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name PETM60 _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # loop_ _struct_ref.id _struct_ref.db_name _struct_ref.db_code _struct_ref.entity_id _struct_ref.pdbx_seq_one_letter_code _struct_ref.pdbx_align_begin _struct_ref.pdbx_db_accession _struct_ref.pdbx_db_isoform 1 PDB 2VC8 1 ? ? 2VC8 ? 2 UNP EDC3_HUMAN 1 ? ? Q96F86 ? # loop_ _struct_ref_seq.align_id _struct_ref_seq.ref_id _struct_ref_seq.pdbx_PDB_id_code _struct_ref_seq.pdbx_strand_id _struct_ref_seq.seq_align_beg _struct_ref_seq.pdbx_seq_align_beg_ins_code _struct_ref_seq.seq_align_end _struct_ref_seq.pdbx_seq_align_end_ins_code _struct_ref_seq.pdbx_db_accession _struct_ref_seq.db_align_beg _struct_ref_seq.pdbx_db_align_beg_ins_code _struct_ref_seq.db_align_end _struct_ref_seq.pdbx_db_align_end_ins_code _struct_ref_seq.pdbx_auth_seq_align_beg _struct_ref_seq.pdbx_auth_seq_align_end 1 1 2VC8 A 1 ? 2 ? 2VC8 -1 ? 0 ? -1 0 2 2 2VC8 A 3 ? 84 ? Q96F86 1 ? 82 ? 1 82 # 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 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.entry_id 2VC8 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 1.77 _exptl_crystal.density_percent_sol 30.6 _exptl_crystal.description NONE # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 4.1 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details '40 MM NA-PROPIONATE, 20 MM NA-CACODYLATE, 40 MM BIS-TRIS-PROPANE, PH=4.1, 32% PEG1500' # _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 MARRESEARCH _diffrn_detector.pdbx_collection_date 2007-03-09 _diffrn_detector.details MIRRORS # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator SI111 _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0500 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'MPG/DESY, HAMBURG BEAMLINE BW6' _diffrn_source.pdbx_synchrotron_site 'MPG/DESY, HAMBURG' _diffrn_source.pdbx_synchrotron_beamline BW6 _diffrn_source.pdbx_wavelength 1.0500 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2VC8 _reflns.observed_criterion_sigma_I . _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 18.70 _reflns.d_resolution_high 1.31 _reflns.number_obs 15783 _reflns.number_all ? _reflns.percent_possible_obs 98.6 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 15.50 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 12.9 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.31 _reflns_shell.d_res_low 1.33 _reflns_shell.percent_possible_all 99.8 _reflns_shell.Rmerge_I_obs 0.28 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.70 _reflns_shell.pdbx_redundancy 3.4 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2VC8 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 14787 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F ? _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low 18.65 _refine.ls_d_res_high 1.31 _refine.ls_percent_reflns_obs 97.3 _refine.ls_R_factor_obs 0.198 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.196 _refine.ls_R_factor_R_free 0.231 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 4.900 _refine.ls_number_reflns_R_free 758 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.967 _refine.correlation_coeff_Fo_to_Fc_free 0.954 _refine.B_iso_mean 18.30 _refine.aniso_B[1][1] -0.54000 _refine.aniso_B[2][2] -0.54000 _refine.aniso_B[3][3] 0.81000 _refine.aniso_B[1][2] -0.27000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 'BABINET MODEL WITH MASK' _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_solvent_vdw_probe_radii 1.20 _refine.pdbx_solvent_ion_probe_radii 0.80 _refine.pdbx_solvent_shrinkage_radii 0.80 _refine.pdbx_ls_cross_valid_method THROUGHOUT _refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct SAD _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD' _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details RANDOM _refine.pdbx_overall_ESU_R 0.071 _refine.pdbx_overall_ESU_R_Free 0.066 _refine.overall_SU_ML 0.049 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 2.467 _refine.overall_SU_R_Cruickshank_DPI ? _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 541 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 54 _refine_hist.number_atoms_total 595 _refine_hist.d_res_high 1.31 _refine_hist.d_res_low 18.65 # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number _refine_ls_restr.pdbx_refine_id _refine_ls_restr.pdbx_restraint_function r_bond_refined_d 0.019 0.022 ? 632 'X-RAY DIFFRACTION' ? r_bond_other_d 0.003 0.020 ? 426 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.752 1.973 ? 882 'X-RAY DIFFRACTION' ? r_angle_other_deg 1.020 3.000 ? 1070 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 6.084 5.000 ? 96 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 32.049 25.000 ? 26 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 12.702 15.000 ? 114 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 14.732 15.000 ? 4 'X-RAY DIFFRACTION' ? r_chiral_restr 0.114 0.200 ? 108 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.009 0.020 ? 732 'X-RAY DIFFRACTION' ? r_gen_planes_other 0.002 0.020 ? 119 'X-RAY DIFFRACTION' ? r_nbd_refined 0.205 0.200 ? 118 'X-RAY DIFFRACTION' ? r_nbd_other 0.209 0.200 ? 438 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.167 0.200 ? 324 'X-RAY DIFFRACTION' ? r_nbtor_other 0.087 0.200 ? 359 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.186 0.200 ? 41 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_vdw_refined 0.243 0.200 ? 11 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other 0.212 0.200 ? 39 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.177 0.200 ? 7 'X-RAY DIFFRACTION' ? r_symmetry_hbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_metal_ion_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcbond_it 6.276 24.000 ? 545 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 6.721 32.000 ? 672 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 7.773 48.000 ? 278 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 9.185 72.000 ? 197 'X-RAY DIFFRACTION' ? r_scangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_refined ? ? ? ? 'X-RAY DIFFRACTION' ? r_long_range_B_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_rigid_bond_restr ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_free ? ? ? ? 'X-RAY DIFFRACTION' ? r_sphericity_bonded ? ? ? ? 'X-RAY DIFFRACTION' ? # _refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION' _refine_ls_shell.pdbx_total_number_of_bins_used 20 _refine_ls_shell.d_res_high 1.31 _refine_ls_shell.d_res_low 1.34 _refine_ls_shell.number_reflns_R_work 1109 _refine_ls_shell.R_factor_R_work 0.3130 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.3830 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 52 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2VC8 _struct.title 'Crystal structure of the LSm domain of human EDC3 (enhancer of decapping 3)' _struct.pdbx_descriptor 'ENHANCER OF MRNA-DECAPPING PROTEIN 3' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2VC8 _struct_keywords.pdbx_keywords 'PROTEIN BINDING' _struct_keywords.text 'P-BODY COMPONENT, ENHANCER OF MRNA DECAPPING, RNA, CYTOPLASM, SM-LIKE PROTEIN, PROTEIN-BINDING, PROTEIN BINDING' # 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 ? # _struct_biol.id 1 # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id 1 _struct_conf.beg_label_comp_id GLY _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 59 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ILE _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 61 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLY _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 57 _struct_conf.end_auth_comp_id ILE _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 59 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 3 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 5 ? AB ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA 1 2 ? anti-parallel AA 2 3 ? anti-parallel AA 3 4 ? anti-parallel AA 4 5 ? anti-parallel AB 1 2 ? anti-parallel AB 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA 1 VAL A 47 ? LYS A 48 ? VAL A 45 LYS A 46 AA 2 THR A 36 ? HIS A 44 ? THR A 34 HIS A 42 AA 3 VAL A 22 ? ASP A 31 ? VAL A 20 ASP A 29 AA 4 ILE A 11 ? ASN A 15 ? ILE A 9 ASN A 13 AA 5 GLU A 63 ? GLU A 68 ? GLU A 61 GLU A 66 AB 1 VAL A 47 ? LYS A 48 ? VAL A 45 LYS A 46 AB 2 THR A 36 ? HIS A 44 ? THR A 34 HIS A 42 AB 3 GLU A 53 ? ARG A 57 ? GLU A 51 ARG A 55 # 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 AA 1 2 N VAL A 47 ? N VAL A 45 O HIS A 44 ? O HIS A 42 AA 2 3 N PHE A 43 ? N PHE A 41 O GLN A 24 ? O GLN A 22 AA 3 4 N GLY A 25 ? N GLY A 23 O VAL A 12 ? O VAL A 10 AA 4 5 N ASN A 15 ? N ASN A 13 O GLU A 63 ? O GLU A 61 AB 1 2 N VAL A 47 ? N VAL A 45 O HIS A 44 ? O HIS A 42 AB 2 3 N LEU A 39 ? N LEU A 37 O VAL A 54 ? O VAL A 52 # _database_PDB_matrix.entry_id 2VC8 _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 2VC8 _atom_sites.fract_transf_matrix[1][1] 0.026810 _atom_sites.fract_transf_matrix[1][2] 0.015478 _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] 0.030957 _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] 0.012625 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # loop_ _atom_type.symbol C N O 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 ? ? ? A . n A 1 2 ALA 2 0 ? ? ? A . n A 1 3 MET 3 1 ? ? ? A . n A 1 4 ALA 4 2 ? ? ? A . n A 1 5 THR 5 3 3 THR THR A . n A 1 6 ASP 6 4 4 ASP ASP A . n A 1 7 TRP 7 5 5 TRP TRP A . n A 1 8 LEU 8 6 6 LEU LEU A . n A 1 9 GLY 9 7 7 GLY GLY A . n A 1 10 SER 10 8 8 SER SER A . n A 1 11 ILE 11 9 9 ILE ILE A . n A 1 12 VAL 12 10 10 VAL VAL A . n A 1 13 SER 13 11 11 SER SER A . n A 1 14 ILE 14 12 12 ILE ILE A . n A 1 15 ASN 15 13 13 ASN ASN A . n A 1 16 CYS 16 14 14 CYS CYS A . n A 1 17 GLY 17 15 15 GLY GLY A . n A 1 18 ASP 18 16 16 ASP ASP A . n A 1 19 SER 19 17 17 SER SER A . n A 1 20 LEU 20 18 18 LEU LEU A . n A 1 21 GLY 21 19 19 GLY GLY A . n A 1 22 VAL 22 20 20 VAL VAL A . n A 1 23 TYR 23 21 21 TYR TYR A . n A 1 24 GLN 24 22 22 GLN GLN A . n A 1 25 GLY 25 23 23 GLY GLY A . n A 1 26 ARG 26 24 24 ARG ARG A . n A 1 27 VAL 27 25 25 VAL VAL A . n A 1 28 SER 28 26 26 SER SER A . n A 1 29 ALA 29 27 27 ALA ALA A . n A 1 30 VAL 30 28 28 VAL VAL A . n A 1 31 ASP 31 29 29 ASP ASP A . n A 1 32 GLN 32 30 30 GLN GLN A . n A 1 33 VAL 33 31 31 VAL VAL A . n A 1 34 SER 34 32 32 SER SER A . n A 1 35 GLN 35 33 33 GLN GLN A . n A 1 36 THR 36 34 34 THR THR A . n A 1 37 ILE 37 35 35 ILE ILE A . n A 1 38 SER 38 36 36 SER SER A . n A 1 39 LEU 39 37 37 LEU LEU A . n A 1 40 THR 40 38 38 THR THR A . n A 1 41 ARG 41 39 39 ARG ARG A . n A 1 42 PRO 42 40 40 PRO PRO A . n A 1 43 PHE 43 41 41 PHE PHE A . n A 1 44 HIS 44 42 42 HIS HIS A . n A 1 45 ASN 45 43 43 ASN ASN A . n A 1 46 GLY 46 44 44 GLY GLY A . n A 1 47 VAL 47 45 45 VAL VAL A . n A 1 48 LYS 48 46 46 LYS LYS A . n A 1 49 CYS 49 47 47 CYS CYS A . n A 1 50 LEU 50 48 48 LEU LEU A . n A 1 51 VAL 51 49 49 VAL VAL A . n A 1 52 PRO 52 50 50 PRO PRO A . n A 1 53 GLU 53 51 51 GLU GLU A . n A 1 54 VAL 54 52 52 VAL VAL A . n A 1 55 THR 55 53 53 THR THR A . n A 1 56 PHE 56 54 54 PHE PHE A . n A 1 57 ARG 57 55 55 ARG ARG A . n A 1 58 ALA 58 56 56 ALA ALA A . n A 1 59 GLY 59 57 57 GLY GLY A . n A 1 60 ASP 60 58 58 ASP ASP A . n A 1 61 ILE 61 59 59 ILE ILE A . n A 1 62 THR 62 60 60 THR THR A . n A 1 63 GLU 63 61 61 GLU GLU A . n A 1 64 LEU 64 62 62 LEU LEU A . n A 1 65 LYS 65 63 63 LYS LYS A . n A 1 66 ILE 66 64 64 ILE ILE A . n A 1 67 LEU 67 65 65 LEU LEU A . n A 1 68 GLU 68 66 66 GLU GLU A . n A 1 69 ILE 69 67 67 ILE ILE A . n A 1 70 PRO 70 68 68 PRO PRO A . n A 1 71 GLY 71 69 69 GLY GLY A . n A 1 72 PRO 72 70 70 PRO PRO A . n A 1 73 GLY 73 71 71 GLY GLY A . n A 1 74 ASP 74 72 72 ASP ASP A . n A 1 75 ASN 75 73 73 ASN ASN A . n A 1 76 GLN 76 74 74 GLN GLN A . n A 1 77 HIS 77 75 ? ? ? A . n A 1 78 PHE 78 76 ? ? ? A . n A 1 79 GLY 79 77 ? ? ? A . n A 1 80 ASP 80 78 ? ? ? A . n A 1 81 LEU 81 79 ? ? ? A . n A 1 82 HIS 82 80 ? ? ? A . n A 1 83 GLN 83 81 ? ? ? A . n A 1 84 THR 84 82 ? ? ? 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 HOH 1 2001 2001 HOH HOH A . B 2 HOH 2 2002 2002 HOH HOH A . B 2 HOH 3 2003 2003 HOH HOH A . B 2 HOH 4 2004 2004 HOH HOH A . B 2 HOH 5 2005 2005 HOH HOH A . B 2 HOH 6 2006 2006 HOH HOH A . B 2 HOH 7 2007 2007 HOH HOH A . B 2 HOH 8 2008 2008 HOH HOH A . B 2 HOH 9 2009 2009 HOH HOH A . B 2 HOH 10 2010 2010 HOH HOH A . B 2 HOH 11 2011 2011 HOH HOH A . B 2 HOH 12 2012 2012 HOH HOH A . B 2 HOH 13 2013 2013 HOH HOH A . B 2 HOH 14 2014 2014 HOH HOH A . B 2 HOH 15 2015 2015 HOH HOH A . B 2 HOH 16 2016 2016 HOH HOH A . B 2 HOH 17 2017 2017 HOH HOH A . B 2 HOH 18 2018 2018 HOH HOH A . B 2 HOH 19 2019 2019 HOH HOH A . B 2 HOH 20 2020 2020 HOH HOH A . B 2 HOH 21 2021 2021 HOH HOH A . B 2 HOH 22 2022 2022 HOH HOH A . B 2 HOH 23 2023 2023 HOH HOH A . B 2 HOH 24 2024 2024 HOH HOH A . B 2 HOH 25 2025 2025 HOH HOH A . B 2 HOH 26 2026 2026 HOH HOH A . B 2 HOH 27 2027 2027 HOH HOH A . B 2 HOH 28 2028 2028 HOH HOH A . B 2 HOH 29 2029 2029 HOH HOH A . B 2 HOH 30 2030 2030 HOH HOH A . B 2 HOH 31 2031 2031 HOH HOH A . B 2 HOH 32 2032 2032 HOH HOH A . B 2 HOH 33 2033 2033 HOH HOH A . B 2 HOH 34 2034 2034 HOH HOH A . B 2 HOH 35 2035 2035 HOH HOH A . B 2 HOH 36 2036 2036 HOH HOH A . B 2 HOH 37 2037 2037 HOH HOH A . B 2 HOH 38 2038 2038 HOH HOH A . B 2 HOH 39 2039 2039 HOH HOH A . B 2 HOH 40 2040 2040 HOH HOH A . B 2 HOH 41 2041 2041 HOH HOH A . B 2 HOH 42 2042 2042 HOH HOH A . B 2 HOH 43 2043 2043 HOH HOH A . B 2 HOH 44 2044 2044 HOH HOH A . B 2 HOH 45 2045 2045 HOH HOH A . B 2 HOH 46 2046 2046 HOH HOH A . B 2 HOH 47 2047 2047 HOH HOH A . B 2 HOH 48 2048 2048 HOH HOH A . B 2 HOH 49 2049 2049 HOH HOH A . B 2 HOH 50 2050 2050 HOH HOH A . B 2 HOH 51 2051 2051 HOH HOH A . B 2 HOH 52 2052 2052 HOH HOH A . B 2 HOH 53 2053 2053 HOH HOH A . B 2 HOH 54 2054 2054 HOH HOH A . # _pdbx_struct_assembly.id 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.method_details PQS _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 # _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 2011-05-08 3 'Structure model' 1 2 2011-07-13 # _pdbx_audit_revision_details.ordinal 1 _pdbx_audit_revision_details.revision_ordinal 1 _pdbx_audit_revision_details.data_content_type 'Structure model' _pdbx_audit_revision_details.provider repository _pdbx_audit_revision_details.type 'Initial release' _pdbx_audit_revision_details.description ? # 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' 'Version format compliance' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal REFMAC refinement 5.2.0019 ? 1 DENZO 'data reduction' . ? 2 SCALEPACK 'data scaling' . ? 3 autoSHARP phasing . ? 4 # _pdbx_database_remark.id 700 _pdbx_database_remark.text ; SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. ; # _pdbx_entry_details.entry_id 2VC8 _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ;THE CRYSTALLIZED SEQUENCE CORRESPONDS TO RESIDUES 1-82 OF HUMAN EDC3 PLUS TWO N-TERMINAL RESIDUES (GA) REMAINING FROM THE PURIFICATION TAG ; # _pdbx_validate_close_contact.id 1 _pdbx_validate_close_contact.PDB_model_num 1 _pdbx_validate_close_contact.auth_atom_id_1 OG _pdbx_validate_close_contact.auth_asym_id_1 A _pdbx_validate_close_contact.auth_comp_id_1 SER _pdbx_validate_close_contact.auth_seq_id_1 17 _pdbx_validate_close_contact.PDB_ins_code_1 ? _pdbx_validate_close_contact.label_alt_id_1 A _pdbx_validate_close_contact.auth_atom_id_2 O _pdbx_validate_close_contact.auth_asym_id_2 A _pdbx_validate_close_contact.auth_comp_id_2 HOH _pdbx_validate_close_contact.auth_seq_id_2 2008 _pdbx_validate_close_contact.PDB_ins_code_2 ? _pdbx_validate_close_contact.label_alt_id_2 ? _pdbx_validate_close_contact.dist 2.15 # _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 39 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 A _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 39 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 A _pdbx_validate_rmsd_angle.auth_atom_id_3 NH2 _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 39 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 A _pdbx_validate_rmsd_angle.angle_value 116.99 _pdbx_validate_rmsd_angle.angle_target_value 120.30 _pdbx_validate_rmsd_angle.angle_deviation -3.31 _pdbx_validate_rmsd_angle.angle_standard_deviation 0.50 _pdbx_validate_rmsd_angle.linker_flag N # _pdbx_validate_torsion.id 1 _pdbx_validate_torsion.PDB_model_num 1 _pdbx_validate_torsion.auth_comp_id ARG _pdbx_validate_torsion.auth_asym_id A _pdbx_validate_torsion.auth_seq_id 39 _pdbx_validate_torsion.PDB_ins_code ? _pdbx_validate_torsion.label_alt_id ? _pdbx_validate_torsion.phi 35.72 _pdbx_validate_torsion.psi 58.64 # 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 GLY -1 ? A GLY 1 2 1 Y 1 A ALA 0 ? A ALA 2 3 1 Y 1 A MET 1 ? A MET 3 4 1 Y 1 A ALA 2 ? A ALA 4 5 1 Y 1 A HIS 75 ? A HIS 77 6 1 Y 1 A PHE 76 ? A PHE 78 7 1 Y 1 A GLY 77 ? A GLY 79 8 1 Y 1 A ASP 78 ? A ASP 80 9 1 Y 1 A LEU 79 ? A LEU 81 10 1 Y 1 A HIS 80 ? A HIS 82 11 1 Y 1 A GLN 81 ? A GLN 83 12 1 Y 1 A THR 82 ? A THR 84 # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name water _pdbx_entity_nonpoly.comp_id HOH #