data_2VP7 # _entry.id 2VP7 # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.308 _audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic # loop_ _database_2.database_id _database_2.database_code PDB 2VP7 PDBE EBI-35447 WWPDB D_1290035447 # loop_ _pdbx_database_related.db_name _pdbx_database_related.db_id _pdbx_database_related.content_type _pdbx_database_related.details PDB 2VPG unspecified 'DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX' PDB 2VPE unspecified 'DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX' PDB 2VPB unspecified 'DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX' PDB 2VPD unspecified 'DECODING OF METHYLATED HISTONE H3 TAIL BY THE PYGO-BCL9 WNT SIGNALING COMPLEX' # _pdbx_database_status.status_code REL _pdbx_database_status.entry_id 2VP7 _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.SG_entry . _pdbx_database_status.recvd_initial_deposition_date 2008-02-26 _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 'Fiedler, M.' 1 'Sanchez-Barrena, M.J.' 2 'Nekrasov, M.' 3 'Mieszczanek, J.' 4 'Rybin, V.' 5 'Muller, J.' 6 'Evans, P.' 7 'Bienz, M.' 8 # _citation.id primary _citation.title 'Decoding of Methylated Histone H3 Tail by the Pygo- Bcl9 Wnt Signaling Complex.' _citation.journal_abbrev Mol.Cell _citation.journal_volume 30 _citation.page_first 507 _citation.page_last ? _citation.year 2008 _citation.journal_id_ASTM MOCEFL _citation.country US _citation.journal_id_ISSN 1097-2765 _citation.journal_id_CSD 2168 _citation.book_publisher ? _citation.pdbx_database_id_PubMed 18498752 _citation.pdbx_database_id_DOI 10.1016/J.MOLCEL.2008.03.011 # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Fiedler, M.' 1 ? primary 'Sanchez-Barrena, M.J.' 2 ? primary 'Nekrasov, M.' 3 ? primary 'Mieszczanek, J.' 4 ? primary 'Rybin, V.' 5 ? primary 'Muller, J.' 6 ? primary 'Evans, P.' 7 ? primary 'Bienz, M.' 8 ? # _cell.entry_id 2VP7 _cell.length_a 32.650 _cell.length_b 72.060 _cell.length_c 91.810 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VP7 _symmetry.space_group_name_H-M 'I 2 2 2' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 # 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 'PYGOPUS HOMOLOG 1' 7661.530 1 ? YES 'PHD DOMAIN, RESIDUES 333-402' ? 2 polymer man 'B-CELL CLL/LYMPHOMA 9 PROTEIN' 3556.132 1 ? ? 'HD1 DOMAIN, RESIDUES 174-205' ? 3 non-polymer syn 'SULFATE ION' 96.063 3 ? ? ? ? 4 non-polymer syn 'ZINC ION' 65.409 2 ? ? ? ? 5 water nat water 18.015 99 ? ? ? ? # loop_ _entity_name_com.entity_id _entity_name_com.name 1 HPYGO1 2 'B-CELL LYMPHOMA 9 PROTEIN, BCL-9, PROTEIN LEGLESS HOMOLOG, BCL9' # loop_ _entity_poly.entity_id _entity_poly.type _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier 1 'polypeptide(L)' no no MGHSSSDPVYPCGICTNEVNDDQDAILCEASCQKFFHRICTGMTETAYGLLTAEASAVWGCDTCMADKDVQ MGHSSSDPVYPCGICTNEVNDDQDAILCEASCQKFFHRICTGMTETAYGLLTAEASAVWGCDTCMADKDVQ A ? 2 'polypeptide(L)' no no AAKVVYVFSTEMANKAAEAVLKGQVETIVSFHI AAKVVYVFSTEMANKAAEAVLKGQVETIVSFHI B ? # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET n 1 2 GLY n 1 3 HIS n 1 4 SER n 1 5 SER n 1 6 SER n 1 7 ASP n 1 8 PRO n 1 9 VAL n 1 10 TYR n 1 11 PRO n 1 12 CYS n 1 13 GLY n 1 14 ILE n 1 15 CYS n 1 16 THR n 1 17 ASN n 1 18 GLU n 1 19 VAL n 1 20 ASN n 1 21 ASP n 1 22 ASP n 1 23 GLN n 1 24 ASP n 1 25 ALA n 1 26 ILE n 1 27 LEU n 1 28 CYS n 1 29 GLU n 1 30 ALA n 1 31 SER n 1 32 CYS n 1 33 GLN n 1 34 LYS n 1 35 PHE n 1 36 PHE n 1 37 HIS n 1 38 ARG n 1 39 ILE n 1 40 CYS n 1 41 THR n 1 42 GLY n 1 43 MET n 1 44 THR n 1 45 GLU n 1 46 THR n 1 47 ALA n 1 48 TYR n 1 49 GLY n 1 50 LEU n 1 51 LEU n 1 52 THR n 1 53 ALA n 1 54 GLU n 1 55 ALA n 1 56 SER n 1 57 ALA n 1 58 VAL n 1 59 TRP n 1 60 GLY n 1 61 CYS n 1 62 ASP n 1 63 THR n 1 64 CYS n 1 65 MET n 1 66 ALA n 1 67 ASP n 1 68 LYS n 1 69 ASP n 1 70 VAL n 1 71 GLN n 2 1 ALA n 2 2 ALA n 2 3 LYS n 2 4 VAL n 2 5 VAL n 2 6 TYR n 2 7 VAL n 2 8 PHE n 2 9 SER n 2 10 THR n 2 11 GLU n 2 12 MET n 2 13 ALA n 2 14 ASN n 2 15 LYS n 2 16 ALA n 2 17 ALA n 2 18 GLU n 2 19 ALA n 2 20 VAL n 2 21 LEU n 2 22 LYS n 2 23 GLY n 2 24 GLN n 2 25 VAL n 2 26 GLU n 2 27 THR n 2 28 ILE n 2 29 VAL n 2 30 SER n 2 31 PHE n 2 32 HIS n 2 33 ILE n # loop_ _entity_src_gen.entity_id _entity_src_gen.pdbx_src_id _entity_src_gen.pdbx_alt_source_flag _entity_src_gen.pdbx_seq_type _entity_src_gen.pdbx_beg_seq_num _entity_src_gen.pdbx_end_seq_num _entity_src_gen.gene_src_common_name _entity_src_gen.gene_src_genus _entity_src_gen.pdbx_gene_src_gene _entity_src_gen.gene_src_species _entity_src_gen.gene_src_strain _entity_src_gen.gene_src_tissue _entity_src_gen.gene_src_tissue_fraction _entity_src_gen.gene_src_details _entity_src_gen.pdbx_gene_src_fragment _entity_src_gen.pdbx_gene_src_scientific_name _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id _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 _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id _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 _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 _entity_src_gen.plasmid_details _entity_src_gen.pdbx_description 1 1 sample ? ? ? HUMAN ? ? ? ? ? ? ? ? 'HOMO SAPIENS' 9606 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 511693 ? ? ? ? ? ? BL21 'CODONPLUS(DE3)-RIL' ? ? ? ? ? ? ? 'BI-CISTRONIC EXPRESSION VECTOR' ? ? ? ? ? 2 1 sample ? ? ? HUMAN ? ? ? ? ? ? ? ? 'HOMO SAPIENS' 9606 ? ? ? ? ? ? ? ? 'ESCHERICHIA COLI' 511693 ? ? ? ? ? ? BL21 'CODONPLUS(DE3)-RIL' ? ? ? ? ? ? ? 'BI-CISTRONIC EXPRESSION VECTOR' ? ? ? ? ? # 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 2VP7 1 ? ? 2VP7 ? 2 UNP PYGO1_HUMAN 1 ? ? Q9Y3Y4 ? 3 PDB 2VP7 2 ? ? 2VP7 ? 4 UNP BCL9_HUMAN 2 ? ? O00512 ? # 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 2VP7 A 1 ? 1 ? 2VP7 332 ? 332 ? 332 332 2 2 2VP7 A 2 ? 71 ? Q9Y3Y4 333 ? 402 ? 333 402 3 3 2VP7 B 1 ? 1 ? 2VP7 173 ? 173 ? 173 173 4 4 2VP7 B 2 ? 33 ? O00512 174 ? 205 ? 174 205 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 2VP7 _struct_ref_seq_dif.mon_id PHE _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 35 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code Q9Y3Y4 _struct_ref_seq_dif.db_mon_id TRP _struct_ref_seq_dif.pdbx_seq_db_seq_num 366 _struct_ref_seq_dif.details 'engineered mutation' _struct_ref_seq_dif.pdbx_auth_seq_num 366 _struct_ref_seq_dif.pdbx_ordinal 1 # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093 ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209 ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118 ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103 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 SO4 non-polymer . 'SULFATE ION' ? 'O4 S -2' 96.063 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 ZN non-polymer . 'ZINC ION' ? 'Zn 2' 65.409 # _exptl.entry_id 2VP7 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number 1 # _exptl_crystal.id 1 _exptl_crystal.density_meas ? _exptl_crystal.density_Matthews 2.06 _exptl_crystal.density_percent_sol 40.37 _exptl_crystal.description NONE _exptl_crystal.preparation ? # _exptl_crystal_grow.crystal_id 1 _exptl_crystal_grow.method 'VAPOR DIFFUSION, HANGING DROP' _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details ? _exptl_crystal_grow.pH 8 _exptl_crystal_grow.pdbx_pH_range ? _exptl_crystal_grow.pdbx_details ;CRYSTALS WERE GROWN USING THE HANGING-DROP VAPOUR-DIFFUSION TECHNIQUE. CRYSTALLIZATION SOLUTION: 1.7M (NH4)2SO4, 100MM TRIS PH7.5, 200MM NACL, pH 8 ; # _diffrn.id 1 _diffrn.ambient_temp 100 _diffrn.ambient_temp_details ? _diffrn.crystal_id 1 _diffrn.pdbx_serial_crystal_experiment ? # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector CCD _diffrn_detector.type 'ADSC CCD' _diffrn_detector.pdbx_collection_date 2007-06-16 _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator 'SINGLE CRYSTAL, SI(111)' _diffrn_radiation.pdbx_diffrn_protocol MAD _diffrn_radiation.pdbx_scattering_type x-ray # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.0000 _diffrn_radiation_wavelength.wt 1.0 # _diffrn_source.diffrn_id 1 _diffrn_source.source SYNCHROTRON _diffrn_source.type 'ESRF BEAMLINE ID23-1' _diffrn_source.pdbx_synchrotron_site ESRF _diffrn_source.pdbx_synchrotron_beamline ID23-1 _diffrn_source.pdbx_wavelength 1.0000 _diffrn_source.pdbx_wavelength_list ? # _reflns.pdbx_diffrn_id 1 _reflns.pdbx_ordinal 1 _reflns.entry_id 2VP7 _reflns.observed_criterion_sigma_I 2.0 _reflns.observed_criterion_sigma_F ? _reflns.d_resolution_low 24.96 _reflns.d_resolution_high 1.65 _reflns.number_obs 12608 _reflns.number_all ? _reflns.percent_possible_obs 99.6 _reflns.pdbx_Rmerge_I_obs 0.05 _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_sigmaI 21.70 _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy 6.8 # _reflns_shell.pdbx_diffrn_id 1 _reflns_shell.pdbx_ordinal 1 _reflns_shell.d_res_high 1.65 _reflns_shell.d_res_low 1.74 _reflns_shell.percent_possible_all 99.6 _reflns_shell.Rmerge_I_obs 0.38 _reflns_shell.pdbx_Rsym_value ? _reflns_shell.meanI_over_sigI_obs 4.70 _reflns_shell.pdbx_redundancy 7.0 # _refine.pdbx_refine_id 'X-RAY DIFFRACTION' _refine.entry_id 2VP7 _refine.pdbx_diffrn_id 1 _refine.pdbx_TLS_residual_ADP_flag ? _refine.ls_number_reflns_obs 12608 _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 56.70 _refine.ls_d_res_high 1.65 _refine.ls_percent_reflns_obs 98.5 _refine.ls_R_factor_obs 0.220 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work 0.218 _refine.ls_R_factor_R_free 0.267 _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free 5.000 _refine.ls_number_reflns_R_free 658 _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.correlation_coeff_Fo_to_Fc 0.947 _refine.correlation_coeff_Fo_to_Fc_free 0.928 _refine.B_iso_mean 28.70 _refine.aniso_B[1][1] 0.81000 _refine.aniso_B[2][2] -0.55000 _refine.aniso_B[3][3] -0.26000 _refine.aniso_B[1][2] 0.00000 _refine.aniso_B[1][3] 0.00000 _refine.aniso_B[2][3] 0.00000 _refine.solvent_model_details 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. THE ZN(II) NUMBER 2 AND ITS BINDING RESIDUES SHOW CERTAIN DISORDER' _refine.pdbx_starting_model NONE _refine.pdbx_method_to_determine_struct MAD _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 0.114 _refine.pdbx_overall_ESU_R_Free 0.119 _refine.overall_SU_ML 0.075 _refine.pdbx_overall_phase_error ? _refine.overall_SU_B 2.111 _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 736 _refine_hist.pdbx_number_atoms_nucleic_acid 0 _refine_hist.pdbx_number_atoms_ligand 17 _refine_hist.number_atoms_solvent 99 _refine_hist.number_atoms_total 852 _refine_hist.d_res_high 1.65 _refine_hist.d_res_low 56.70 # 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 0.012 0.022 ? 798 'X-RAY DIFFRACTION' ? r_bond_other_d ? ? ? ? 'X-RAY DIFFRACTION' ? r_angle_refined_deg 1.372 1.955 ? 1091 'X-RAY DIFFRACTION' ? r_angle_other_deg ? ? ? ? 'X-RAY DIFFRACTION' ? r_dihedral_angle_1_deg 5.350 5.000 ? 107 'X-RAY DIFFRACTION' ? r_dihedral_angle_2_deg 34.169 25.938 ? 32 'X-RAY DIFFRACTION' ? r_dihedral_angle_3_deg 13.644 15.000 ? 130 'X-RAY DIFFRACTION' ? r_dihedral_angle_4_deg 12.050 15.000 ? 1 'X-RAY DIFFRACTION' ? r_chiral_restr 0.103 0.200 ? 126 'X-RAY DIFFRACTION' ? r_gen_planes_refined 0.005 0.020 ? 593 'X-RAY DIFFRACTION' ? r_gen_planes_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbd_refined 0.213 0.200 ? 373 'X-RAY DIFFRACTION' ? r_nbd_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_nbtor_refined 0.302 0.200 ? 554 'X-RAY DIFFRACTION' ? r_nbtor_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_xyhbond_nbd_refined 0.152 0.200 ? 67 '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 0.159 0.200 ? 36 'X-RAY DIFFRACTION' ? r_symmetry_vdw_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_symmetry_hbond_refined 0.198 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 1.107 1.500 ? 522 'X-RAY DIFFRACTION' ? r_mcbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_mcangle_it 1.840 2.000 ? 825 'X-RAY DIFFRACTION' ? r_mcangle_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scbond_it 2.520 3.000 ? 309 'X-RAY DIFFRACTION' ? r_scbond_other ? ? ? ? 'X-RAY DIFFRACTION' ? r_scangle_it 3.527 4.500 ? 262 '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 1.65 _refine_ls_shell.d_res_low 1.69 _refine_ls_shell.number_reflns_R_work 839 _refine_ls_shell.R_factor_R_work 0.2580 _refine_ls_shell.percent_reflns_obs ? _refine_ls_shell.R_factor_R_free 0.2900 _refine_ls_shell.R_factor_R_free_error ? _refine_ls_shell.percent_reflns_R_free ? _refine_ls_shell.number_reflns_R_free 45 _refine_ls_shell.number_reflns_all ? _refine_ls_shell.R_factor_all ? # _struct.entry_id 2VP7 _struct.title 'Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex' _struct.pdbx_descriptor 'PYGOPUS HOMOLOG 1, B-CELL CLL/LYMPHOMA 9 PROTEIN' _struct.pdbx_model_details ? _struct.pdbx_CASP_flag ? _struct.pdbx_model_type_details ? # _struct_keywords.entry_id 2VP7 _struct_keywords.pdbx_keywords 'GENE REGULATION' _struct_keywords.text ;GENE REGULATION, WNT SIGNALING PATHWAY, WNT SIGNALING COMPLEX, CHROMOSOMAL REARRANGEMENT, SIGNALING PROTEIN, PROTO-ONCOGENE, PHOSPHOPROTEIN, PYGO PHD DOMAIN, BCL9 HD1 DOMAIN, HISTONE H3K4ME2 TAIL, ZINC, NUCLEUS, ZINC-FINGER, METAL-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 ? C N N 3 ? D N N 4 ? E N N 4 ? F N N 3 ? G N N 3 ? H N N 5 ? I N N 5 ? # 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 ARG A 38 ? GLY A 42 ? ARG A 369 GLY A 373 1 ? 5 HELX_P HELX_P2 2 THR A 44 ? GLU A 54 ? THR A 375 GLU A 385 1 ? 11 HELX_P HELX_P3 3 CYS A 61 ? ALA A 66 ? CYS A 392 ALA A 397 1 ? 6 HELX_P HELX_P4 4 SER B 9 ? LYS B 22 ? SER B 181 LYS B 194 1 ? 14 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_label_atom_id _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_label_atom_id _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.details _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc1 metalc ? ? D ZN . ZN ? ? ? 1_555 A CYS 15 SG ? ? A ZN 1399 A CYS 346 1_555 ? ? ? ? ? ? ? 2.413 ? metalc2 metalc ? ? D ZN . ZN ? ? ? 1_555 A CYS 12 SG ? ? A ZN 1399 A CYS 343 1_555 ? ? ? ? ? ? ? 2.315 ? metalc3 metalc ? ? D ZN . ZN ? ? ? 1_555 A HIS 37 ND1 ? ? A ZN 1399 A HIS 368 1_555 ? ? ? ? ? ? ? 1.987 ? metalc4 metalc ? ? D ZN . ZN ? ? ? 1_555 A CYS 40 SG ? ? A ZN 1399 A CYS 371 1_555 ? ? ? ? ? ? ? 2.260 ? metalc5 metalc ? ? E ZN . ZN ? ? ? 1_555 A CYS 61 SG ? ? A ZN 1400 A CYS 392 1_555 ? ? ? ? ? ? ? 2.155 ? metalc6 metalc ? ? E ZN . ZN ? ? ? 1_555 A CYS 28 SG ? ? A ZN 1400 A CYS 359 1_555 ? ? ? ? ? ? ? 2.246 ? metalc7 metalc ? ? E ZN . ZN ? ? ? 1_555 A CYS 32 SG ? ? A ZN 1400 A CYS 363 1_555 ? ? ? ? ? ? ? 2.238 ? # _struct_conn_type.id metalc _struct_conn_type.criteria ? _struct_conn_type.reference ? # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA ? 2 ? AB ? 2 ? # 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 AB 1 2 ? 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 ALA A 25 ? LEU A 27 ? ALA A 356 LEU A 358 AA 2 PHE A 35 ? HIS A 37 ? PHE A 366 HIS A 368 AB 1 ALA A 57 ? TRP A 59 ? ALA A 388 TRP A 390 AB 2 TYR B 6 ? PHE B 8 ? TYR B 178 PHE B 180 # 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 ILE A 26 ? N ILE A 357 O PHE A 36 ? O PHE A 367 AB 1 2 N VAL A 58 ? N VAL A 389 O TYR B 6 ? O TYR B 178 # 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 ? ? ? ? 2 'BINDING SITE FOR RESIDUE SO4 B1206' AC2 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE SO4 A1398' AC3 Software ? ? ? ? 5 'BINDING SITE FOR RESIDUE SO4 B1207' AC4 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A1399' AC5 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE ZN A1400' # 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 2 TYR B 6 ? TYR B 178 . ? 1_555 ? 2 AC1 2 PHE B 31 ? PHE B 203 . ? 1_555 ? 3 AC2 4 HIS A 3 ? HIS A 334 . ? 1_555 ? 4 AC2 4 VAL A 19 ? VAL A 350 . ? 1_555 ? 5 AC2 4 ALA A 25 ? ALA A 356 . ? 1_555 ? 6 AC2 4 PHE A 35 ? PHE A 366 . ? 1_555 ? 7 AC3 5 LYS B 3 ? LYS B 175 . ? 1_555 ? 8 AC3 5 HOH I . ? HOH B 1036 . ? 1_555 ? 9 AC3 5 HOH I . ? HOH B 1037 . ? 1_555 ? 10 AC3 5 HOH I . ? HOH B 1038 . ? 1_555 ? 11 AC3 5 HOH I . ? HOH B 1039 . ? 1_555 ? 12 AC4 4 CYS A 12 ? CYS A 343 . ? 1_555 ? 13 AC4 4 CYS A 15 ? CYS A 346 . ? 1_555 ? 14 AC4 4 HIS A 37 ? HIS A 368 . ? 1_555 ? 15 AC4 4 CYS A 40 ? CYS A 371 . ? 1_555 ? 16 AC5 4 CYS A 28 ? CYS A 359 . ? 1_555 ? 17 AC5 4 CYS A 32 ? CYS A 363 . ? 1_555 ? 18 AC5 4 CYS A 61 ? CYS A 392 . ? 1_555 ? 19 AC5 4 CYS A 64 ? CYS A 395 . ? 1_555 ? # _database_PDB_matrix.entry_id 2VP7 _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 2VP7 _atom_sites.fract_transf_matrix[1][1] 0.030628 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.013877 _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] 0.010892 _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 ZN # 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 MET 1 332 332 MET MET A . n A 1 2 GLY 2 333 333 GLY GLY A . n A 1 3 HIS 3 334 334 HIS HIS A . n A 1 4 SER 4 335 335 SER SER A . n A 1 5 SER 5 336 336 SER SER A . n A 1 6 SER 6 337 337 SER SER A . n A 1 7 ASP 7 338 338 ASP ASP A . n A 1 8 PRO 8 339 339 PRO PRO A . n A 1 9 VAL 9 340 340 VAL VAL A . n A 1 10 TYR 10 341 341 TYR TYR A . n A 1 11 PRO 11 342 342 PRO PRO A . n A 1 12 CYS 12 343 343 CYS CYS A . n A 1 13 GLY 13 344 344 GLY GLY A . n A 1 14 ILE 14 345 345 ILE ILE A . n A 1 15 CYS 15 346 346 CYS CYS A . n A 1 16 THR 16 347 347 THR THR A . n A 1 17 ASN 17 348 348 ASN ASN A . n A 1 18 GLU 18 349 349 GLU GLU A . n A 1 19 VAL 19 350 350 VAL VAL A . n A 1 20 ASN 20 351 351 ASN ASN A . n A 1 21 ASP 21 352 352 ASP ASP A . n A 1 22 ASP 22 353 353 ASP ASP A . n A 1 23 GLN 23 354 354 GLN GLN A . n A 1 24 ASP 24 355 355 ASP ASP A . n A 1 25 ALA 25 356 356 ALA ALA A . n A 1 26 ILE 26 357 357 ILE ILE A . n A 1 27 LEU 27 358 358 LEU LEU A . n A 1 28 CYS 28 359 359 CYS CYS A . n A 1 29 GLU 29 360 360 GLU GLU A . n A 1 30 ALA 30 361 361 ALA ALA A . n A 1 31 SER 31 362 362 SER SER A . n A 1 32 CYS 32 363 363 CYS CYS A . n A 1 33 GLN 33 364 364 GLN GLN A . n A 1 34 LYS 34 365 365 LYS LYS A . n A 1 35 PHE 35 366 366 PHE PHE A . n A 1 36 PHE 36 367 367 PHE PHE A . n A 1 37 HIS 37 368 368 HIS HIS A . n A 1 38 ARG 38 369 369 ARG ARG A . n A 1 39 ILE 39 370 370 ILE ILE A . n A 1 40 CYS 40 371 371 CYS CYS A . n A 1 41 THR 41 372 372 THR THR A . n A 1 42 GLY 42 373 373 GLY GLY A . n A 1 43 MET 43 374 374 MET MET A . n A 1 44 THR 44 375 375 THR THR A . n A 1 45 GLU 45 376 376 GLU GLU A . n A 1 46 THR 46 377 377 THR THR A . n A 1 47 ALA 47 378 378 ALA ALA A . n A 1 48 TYR 48 379 379 TYR TYR A . n A 1 49 GLY 49 380 380 GLY GLY A . n A 1 50 LEU 50 381 381 LEU LEU A . n A 1 51 LEU 51 382 382 LEU LEU A . n A 1 52 THR 52 383 383 THR THR A . n A 1 53 ALA 53 384 384 ALA ALA A . n A 1 54 GLU 54 385 385 GLU GLU A . n A 1 55 ALA 55 386 386 ALA ALA A . n A 1 56 SER 56 387 387 SER SER A . n A 1 57 ALA 57 388 388 ALA ALA A . n A 1 58 VAL 58 389 389 VAL VAL A . n A 1 59 TRP 59 390 390 TRP TRP A . n A 1 60 GLY 60 391 391 GLY GLY A . n A 1 61 CYS 61 392 392 CYS CYS A . n A 1 62 ASP 62 393 393 ASP ASP A . n A 1 63 THR 63 394 394 THR THR A . n A 1 64 CYS 64 395 395 CYS CYS A . n A 1 65 MET 65 396 396 MET MET A . n A 1 66 ALA 66 397 397 ALA ALA A . n A 1 67 ASP 67 398 ? ? ? A . n A 1 68 LYS 68 399 ? ? ? A . n A 1 69 ASP 69 400 ? ? ? A . n A 1 70 VAL 70 401 ? ? ? A . n A 1 71 GLN 71 402 ? ? ? A . n B 2 1 ALA 1 173 173 ALA ALA B . n B 2 2 ALA 2 174 174 ALA ALA B . n B 2 3 LYS 3 175 175 LYS LYS B . n B 2 4 VAL 4 176 176 VAL VAL B . n B 2 5 VAL 5 177 177 VAL VAL B . n B 2 6 TYR 6 178 178 TYR TYR B . n B 2 7 VAL 7 179 179 VAL VAL B . n B 2 8 PHE 8 180 180 PHE PHE B . n B 2 9 SER 9 181 181 SER SER B . n B 2 10 THR 10 182 182 THR THR B . n B 2 11 GLU 11 183 183 GLU GLU B . n B 2 12 MET 12 184 184 MET MET B . n B 2 13 ALA 13 185 185 ALA ALA B . n B 2 14 ASN 14 186 186 ASN ASN B . n B 2 15 LYS 15 187 187 LYS LYS B . n B 2 16 ALA 16 188 188 ALA ALA B . n B 2 17 ALA 17 189 189 ALA ALA B . n B 2 18 GLU 18 190 190 GLU GLU B . n B 2 19 ALA 19 191 191 ALA ALA B . n B 2 20 VAL 20 192 192 VAL VAL B . n B 2 21 LEU 21 193 193 LEU LEU B . n B 2 22 LYS 22 194 194 LYS LYS B . n B 2 23 GLY 23 195 195 GLY GLY B . n B 2 24 GLN 24 196 196 GLN GLN B . n B 2 25 VAL 25 197 197 VAL VAL B . n B 2 26 GLU 26 198 198 GLU GLU B . n B 2 27 THR 27 199 199 THR THR B . n B 2 28 ILE 28 200 200 ILE ILE B . n B 2 29 VAL 29 201 201 VAL VAL B . n B 2 30 SER 30 202 202 SER SER B . n B 2 31 PHE 31 203 203 PHE PHE B . n B 2 32 HIS 32 204 204 HIS HIS B . n B 2 33 ILE 33 205 205 ILE ILE B . 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 C 3 SO4 1 1398 1398 SO4 SO4 A . D 4 ZN 1 1399 1399 ZN ZN A . E 4 ZN 1 1400 1400 ZN ZN A . F 3 SO4 1 1206 1206 SO4 SO4 B . G 3 SO4 1 1207 1207 SO4 SO4 B . H 5 HOH 1 1001 1001 HOH HOH A . H 5 HOH 2 1002 1002 HOH HOH A . H 5 HOH 3 1003 1003 HOH HOH A . H 5 HOH 4 1004 1004 HOH HOH A . H 5 HOH 5 1005 1005 HOH HOH A . H 5 HOH 6 1006 1006 HOH HOH A . H 5 HOH 7 1007 1007 HOH HOH A . H 5 HOH 8 1008 1008 HOH HOH A . H 5 HOH 9 1009 1009 HOH HOH A . H 5 HOH 10 1010 1010 HOH HOH A . H 5 HOH 11 1011 1011 HOH HOH A . H 5 HOH 12 1012 1012 HOH HOH A . H 5 HOH 13 1013 1013 HOH HOH A . H 5 HOH 14 1014 1014 HOH HOH A . H 5 HOH 15 1015 1015 HOH HOH A . H 5 HOH 16 1016 1016 HOH HOH A . H 5 HOH 17 1017 1017 HOH HOH A . H 5 HOH 18 1018 1018 HOH HOH A . H 5 HOH 19 1019 1019 HOH HOH A . H 5 HOH 20 1020 1020 HOH HOH A . H 5 HOH 21 1021 1021 HOH HOH A . H 5 HOH 22 1022 1022 HOH HOH A . H 5 HOH 23 1023 1023 HOH HOH A . H 5 HOH 24 1024 1024 HOH HOH A . H 5 HOH 25 1025 1025 HOH HOH A . H 5 HOH 26 1026 1026 HOH HOH A . H 5 HOH 27 1027 1027 HOH HOH A . H 5 HOH 28 1028 1028 HOH HOH A . H 5 HOH 29 1029 1029 HOH HOH A . H 5 HOH 30 1030 1030 HOH HOH A . H 5 HOH 31 1031 1031 HOH HOH A . H 5 HOH 32 1032 1032 HOH HOH A . H 5 HOH 33 1033 1033 HOH HOH A . H 5 HOH 34 1034 1034 HOH HOH A . H 5 HOH 35 1035 1035 HOH HOH A . H 5 HOH 36 1036 1036 HOH HOH A . H 5 HOH 37 1037 1037 HOH HOH A . H 5 HOH 38 1038 1038 HOH HOH A . H 5 HOH 39 1039 1039 HOH HOH A . H 5 HOH 40 1040 1040 HOH HOH A . H 5 HOH 41 1041 1041 HOH HOH A . H 5 HOH 42 1042 1042 HOH HOH A . H 5 HOH 43 1043 1043 HOH HOH A . H 5 HOH 44 1044 1044 HOH HOH A . H 5 HOH 45 1045 1045 HOH HOH A . H 5 HOH 46 1046 1046 HOH HOH A . H 5 HOH 47 1047 1047 HOH HOH A . H 5 HOH 48 1048 1048 HOH HOH A . H 5 HOH 49 1049 1049 HOH HOH A . H 5 HOH 50 1050 1050 HOH HOH A . H 5 HOH 51 1051 1051 HOH HOH A . H 5 HOH 52 1052 1052 HOH HOH A . H 5 HOH 53 1053 1053 HOH HOH A . H 5 HOH 54 1054 1054 HOH HOH A . H 5 HOH 55 1055 1055 HOH HOH A . H 5 HOH 56 1056 1056 HOH HOH A . H 5 HOH 57 1057 1057 HOH HOH A . H 5 HOH 58 1058 1058 HOH HOH A . H 5 HOH 59 1059 1059 HOH HOH A . H 5 HOH 60 1060 1060 HOH HOH A . I 5 HOH 1 1001 1001 HOH HOH B . I 5 HOH 2 1002 1002 HOH HOH B . I 5 HOH 3 1003 1003 HOH HOH B . I 5 HOH 4 1004 1004 HOH HOH B . I 5 HOH 5 1005 1005 HOH HOH B . I 5 HOH 6 1006 1006 HOH HOH B . I 5 HOH 7 1007 1007 HOH HOH B . I 5 HOH 8 1008 1008 HOH HOH B . I 5 HOH 9 1009 1009 HOH HOH B . I 5 HOH 10 1010 1010 HOH HOH B . I 5 HOH 11 1011 1011 HOH HOH B . I 5 HOH 12 1012 1012 HOH HOH B . I 5 HOH 13 1013 1013 HOH HOH B . I 5 HOH 14 1014 1014 HOH HOH B . I 5 HOH 15 1015 1015 HOH HOH B . I 5 HOH 16 1016 1016 HOH HOH B . I 5 HOH 17 1017 1017 HOH HOH B . I 5 HOH 18 1018 1018 HOH HOH B . I 5 HOH 19 1019 1019 HOH HOH B . I 5 HOH 20 1020 1020 HOH HOH B . I 5 HOH 21 1021 1021 HOH HOH B . I 5 HOH 22 1022 1022 HOH HOH B . I 5 HOH 23 1023 1023 HOH HOH B . I 5 HOH 24 1024 1024 HOH HOH B . I 5 HOH 25 1025 1025 HOH HOH B . I 5 HOH 26 1026 1026 HOH HOH B . I 5 HOH 27 1027 1027 HOH HOH B . I 5 HOH 28 1028 1028 HOH HOH B . I 5 HOH 29 1029 1029 HOH HOH B . I 5 HOH 30 1030 1030 HOH HOH B . I 5 HOH 31 1031 1031 HOH HOH B . I 5 HOH 32 1032 1032 HOH HOH B . I 5 HOH 33 1033 1033 HOH HOH B . I 5 HOH 34 1034 1034 HOH HOH B . I 5 HOH 35 1035 1035 HOH HOH B . I 5 HOH 36 1036 1036 HOH HOH B . I 5 HOH 37 1037 1037 HOH HOH B . I 5 HOH 38 1038 1038 HOH HOH B . I 5 HOH 39 1039 1039 HOH HOH B . # _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 # _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I # 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)' 1530 ? 1 MORE -13 ? 1 'SSA (A^2)' 7810 ? # _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 # _pdbx_struct_special_symmetry.id 1 _pdbx_struct_special_symmetry.PDB_model_num 1 _pdbx_struct_special_symmetry.auth_asym_id B _pdbx_struct_special_symmetry.auth_comp_id HOH _pdbx_struct_special_symmetry.auth_seq_id 1039 _pdbx_struct_special_symmetry.PDB_ins_code ? _pdbx_struct_special_symmetry.label_asym_id I _pdbx_struct_special_symmetry.label_comp_id HOH _pdbx_struct_special_symmetry.label_seq_id . # loop_ _pdbx_struct_conn_angle.id _pdbx_struct_conn_angle.ptnr1_label_atom_id _pdbx_struct_conn_angle.ptnr1_label_alt_id _pdbx_struct_conn_angle.ptnr1_label_asym_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr1_label_seq_id _pdbx_struct_conn_angle.ptnr1_auth_atom_id _pdbx_struct_conn_angle.ptnr1_auth_asym_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_auth_seq_id _pdbx_struct_conn_angle.ptnr1_PDB_ins_code _pdbx_struct_conn_angle.ptnr1_symmetry _pdbx_struct_conn_angle.ptnr2_label_atom_id _pdbx_struct_conn_angle.ptnr2_label_alt_id _pdbx_struct_conn_angle.ptnr2_label_asym_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr2_label_seq_id _pdbx_struct_conn_angle.ptnr2_auth_atom_id _pdbx_struct_conn_angle.ptnr2_auth_asym_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_auth_seq_id _pdbx_struct_conn_angle.ptnr2_PDB_ins_code _pdbx_struct_conn_angle.ptnr2_symmetry _pdbx_struct_conn_angle.ptnr3_label_atom_id _pdbx_struct_conn_angle.ptnr3_label_alt_id _pdbx_struct_conn_angle.ptnr3_label_asym_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _pdbx_struct_conn_angle.ptnr3_label_seq_id _pdbx_struct_conn_angle.ptnr3_auth_atom_id _pdbx_struct_conn_angle.ptnr3_auth_asym_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_auth_seq_id _pdbx_struct_conn_angle.ptnr3_PDB_ins_code _pdbx_struct_conn_angle.ptnr3_symmetry _pdbx_struct_conn_angle.value _pdbx_struct_conn_angle.value_esd 1 SG ? A CYS 15 ? A CYS 346 ? 1_555 ZN ? D ZN . ? A ZN 1399 ? 1_555 SG ? A CYS 12 ? A CYS 343 ? 1_555 109.6 ? 2 SG ? A CYS 15 ? A CYS 346 ? 1_555 ZN ? D ZN . ? A ZN 1399 ? 1_555 ND1 ? A HIS 37 ? A HIS 368 ? 1_555 99.9 ? 3 SG ? A CYS 12 ? A CYS 343 ? 1_555 ZN ? D ZN . ? A ZN 1399 ? 1_555 ND1 ? A HIS 37 ? A HIS 368 ? 1_555 102.1 ? 4 SG ? A CYS 15 ? A CYS 346 ? 1_555 ZN ? D ZN . ? A ZN 1399 ? 1_555 SG ? A CYS 40 ? A CYS 371 ? 1_555 113.7 ? 5 SG ? A CYS 12 ? A CYS 343 ? 1_555 ZN ? D ZN . ? A ZN 1399 ? 1_555 SG ? A CYS 40 ? A CYS 371 ? 1_555 118.5 ? 6 ND1 ? A HIS 37 ? A HIS 368 ? 1_555 ZN ? D ZN . ? A ZN 1399 ? 1_555 SG ? A CYS 40 ? A CYS 371 ? 1_555 110.9 ? 7 SG ? A CYS 61 ? A CYS 392 ? 1_555 ZN ? E ZN . ? A ZN 1400 ? 1_555 SG ? A CYS 28 ? A CYS 359 ? 1_555 121.9 ? 8 SG ? A CYS 61 ? A CYS 392 ? 1_555 ZN ? E ZN . ? A ZN 1400 ? 1_555 SG ? A CYS 32 ? A CYS 363 ? 1_555 115.7 ? 9 SG ? A CYS 28 ? A CYS 359 ? 1_555 ZN ? E ZN . ? A ZN 1400 ? 1_555 SG ? A CYS 32 ? A CYS 363 ? 1_555 109.3 ? # 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 2008-06-17 2 'Structure model' 1 1 2011-05-08 3 'Structure model' 1 2 2011-07-13 4 'Structure model' 1 3 2019-05-29 # _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' 3 4 'Structure model' 'Data collection' 4 4 'Structure model' 'Experimental preparation' 5 4 'Structure model' Other # loop_ _pdbx_audit_revision_category.ordinal _pdbx_audit_revision_category.revision_ordinal _pdbx_audit_revision_category.data_content_type _pdbx_audit_revision_category.category 1 4 'Structure model' exptl_crystal_grow 2 4 'Structure model' pdbx_database_proc 3 4 'Structure model' pdbx_database_status 4 4 'Structure model' struct_biol # 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' '_exptl_crystal_grow.method' 2 4 'Structure model' '_pdbx_database_status.recvd_author_approval' # loop_ _software.name _software.classification _software.version _software.citation_id _software.pdbx_ordinal _software.date _software.type _software.location _software.language REFMAC refinement 5.3.0037 ? 1 ? ? ? ? MOSFLM 'data reduction' . ? 2 ? ? ? ? SCALA 'data scaling' . ? 3 ? ? ? ? autoSHARP phasing . ? 4 ? ? ? ? # _pdbx_entry_details.entry_id 2VP7 _pdbx_entry_details.compound_details 'ENGINEERED RESIDUE IN CHAIN A, TRP 366 TO PHE' _pdbx_entry_details.source_details ? _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details 'MUTATION W366F' # _pdbx_validate_rmsd_bond.id 1 _pdbx_validate_rmsd_bond.PDB_model_num 1 _pdbx_validate_rmsd_bond.auth_atom_id_1 CB _pdbx_validate_rmsd_bond.auth_asym_id_1 A _pdbx_validate_rmsd_bond.auth_comp_id_1 CYS _pdbx_validate_rmsd_bond.auth_seq_id_1 392 _pdbx_validate_rmsd_bond.PDB_ins_code_1 ? _pdbx_validate_rmsd_bond.label_alt_id_1 ? _pdbx_validate_rmsd_bond.auth_atom_id_2 SG _pdbx_validate_rmsd_bond.auth_asym_id_2 A _pdbx_validate_rmsd_bond.auth_comp_id_2 CYS _pdbx_validate_rmsd_bond.auth_seq_id_2 392 _pdbx_validate_rmsd_bond.PDB_ins_code_2 ? _pdbx_validate_rmsd_bond.label_alt_id_2 ? _pdbx_validate_rmsd_bond.bond_value 1.945 _pdbx_validate_rmsd_bond.bond_target_value 1.818 _pdbx_validate_rmsd_bond.bond_deviation 0.127 _pdbx_validate_rmsd_bond.bond_standard_deviation 0.017 _pdbx_validate_rmsd_bond.linker_flag N # _pdbx_validate_rmsd_angle.id 1 _pdbx_validate_rmsd_angle.PDB_model_num 1 _pdbx_validate_rmsd_angle.auth_atom_id_1 CA _pdbx_validate_rmsd_angle.auth_asym_id_1 A _pdbx_validate_rmsd_angle.auth_comp_id_1 CYS _pdbx_validate_rmsd_angle.auth_seq_id_1 392 _pdbx_validate_rmsd_angle.PDB_ins_code_1 ? _pdbx_validate_rmsd_angle.label_alt_id_1 ? _pdbx_validate_rmsd_angle.auth_atom_id_2 CB _pdbx_validate_rmsd_angle.auth_asym_id_2 A _pdbx_validate_rmsd_angle.auth_comp_id_2 CYS _pdbx_validate_rmsd_angle.auth_seq_id_2 392 _pdbx_validate_rmsd_angle.PDB_ins_code_2 ? _pdbx_validate_rmsd_angle.label_alt_id_2 ? _pdbx_validate_rmsd_angle.auth_atom_id_3 SG _pdbx_validate_rmsd_angle.auth_asym_id_3 A _pdbx_validate_rmsd_angle.auth_comp_id_3 CYS _pdbx_validate_rmsd_angle.auth_seq_id_3 392 _pdbx_validate_rmsd_angle.PDB_ins_code_3 ? _pdbx_validate_rmsd_angle.label_alt_id_3 ? _pdbx_validate_rmsd_angle.angle_value 124.99 _pdbx_validate_rmsd_angle.angle_target_value 114.20 _pdbx_validate_rmsd_angle.angle_deviation 10.79 _pdbx_validate_rmsd_angle.angle_standard_deviation 1.10 _pdbx_validate_rmsd_angle.linker_flag N # loop_ _pdbx_validate_torsion.id _pdbx_validate_torsion.PDB_model_num _pdbx_validate_torsion.auth_comp_id _pdbx_validate_torsion.auth_asym_id _pdbx_validate_torsion.auth_seq_id _pdbx_validate_torsion.PDB_ins_code _pdbx_validate_torsion.label_alt_id _pdbx_validate_torsion.phi _pdbx_validate_torsion.psi 1 1 THR A 347 ? ? 72.60 -6.52 2 1 SER A 362 ? ? -155.81 -53.41 # 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 ASP 398 ? A ASP 67 2 1 Y 1 A LYS 399 ? A LYS 68 3 1 Y 1 A ASP 400 ? A ASP 69 4 1 Y 1 A VAL 401 ? A VAL 70 5 1 Y 1 A GLN 402 ? A GLN 71 # loop_ _pdbx_entity_nonpoly.entity_id _pdbx_entity_nonpoly.name _pdbx_entity_nonpoly.comp_id 3 'SULFATE ION' SO4 4 'ZINC ION' ZN 5 water HOH #