data_6SFT # _entry.id 6SFT # _audit_conform.dict_name mmcif_pdbx.dic _audit_conform.dict_version 5.371 _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 6SFT pdb_00006sft 10.2210/pdb6sft/pdb WWPDB D_1292103582 ? ? # loop_ _pdbx_database_related.db_name _pdbx_database_related.details _pdbx_database_related.db_id _pdbx_database_related.content_type BMRB 'apo ARR_CleD assignments' 27990 unspecified BMRB 'Solution structure of protein ARR_CleD in complex with c-di-GMP' 50001 unspecified # _pdbx_database_status.status_code REL _pdbx_database_status.status_code_sf ? _pdbx_database_status.status_code_mr REL _pdbx_database_status.entry_id 6SFT _pdbx_database_status.recvd_initial_deposition_date 2019-08-02 _pdbx_database_status.SG_entry N _pdbx_database_status.deposit_site PDBE _pdbx_database_status.process_site PDBE _pdbx_database_status.status_code_cs REL _pdbx_database_status.methods_development_category ? _pdbx_database_status.pdb_format_compatible Y _pdbx_database_status.status_code_nmr_data REL # loop_ _audit_author.name _audit_author.pdbx_ordinal _audit_author.identifier_ORCID 'Habazettl, J.' 1 ? 'Hee, C.S.' 2 ? 'Jenal, U.' 3 ? 'Schirmer, T.' 4 ? 'Grzesiek, S.' 5 ? # _citation.abstract ? _citation.abstract_id_CAS ? _citation.book_id_ISBN ? _citation.book_publisher ? _citation.book_publisher_city ? _citation.book_title ? _citation.coordinate_linkage ? _citation.country US _citation.database_id_Medline ? _citation.details ? _citation.id primary _citation.journal_abbrev Proc.Natl.Acad.Sci.USA _citation.journal_id_ASTM PNASA6 _citation.journal_id_CSD 0040 _citation.journal_id_ISSN 1091-6490 _citation.journal_full ? _citation.journal_issue ? _citation.journal_volume 117 _citation.language ? _citation.page_first 17211 _citation.page_last 17220 _citation.title 'Intercepting second-messenger signaling by rationally designed peptides sequestering c-di-GMP.' _citation.year 2020 _citation.database_id_CSD ? _citation.pdbx_database_id_DOI 10.1073/pnas.2001232117 _citation.pdbx_database_id_PubMed 32611811 _citation.unpublished_flag ? # loop_ _citation_author.citation_id _citation_author.name _citation_author.ordinal _citation_author.identifier_ORCID primary 'Hee, C.S.' 1 0000-0002-7697-312X primary 'Habazettl, J.' 2 0000-0002-7976-768X primary 'Schmutz, C.' 3 ? primary 'Schirmer, T.' 4 0000-0001-9512-8346 primary 'Jenal, U.' 5 0000-0002-1637-3376 primary 'Grzesiek, S.' 6 0000-0003-1998-4225 # 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 'Two-component receiver protein CleD' 4174.684 1 ? ? ? 'ARR_CleD is the arginine rich region of CleD, ranging from K140 to S174. It binds intercalated dimeric c-di-GMP' 2 non-polymer syn ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; 690.411 2 ? ? ? ? # _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 SKPREWVEAVAYVGPDRRRFNSADYKGPRKRKADAS _entity_poly.pdbx_seq_one_letter_code_can SKPREWVEAVAYVGPDRRRFNSADYKGPRKRKADAS _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 SER n 1 2 LYS n 1 3 PRO n 1 4 ARG n 1 5 GLU n 1 6 TRP n 1 7 VAL n 1 8 GLU n 1 9 ALA n 1 10 VAL n 1 11 ALA n 1 12 TYR n 1 13 VAL n 1 14 GLY n 1 15 PRO n 1 16 ASP n 1 17 ARG n 1 18 ARG n 1 19 ARG n 1 20 PHE n 1 21 ASN n 1 22 SER n 1 23 ALA n 1 24 ASP n 1 25 TYR n 1 26 LYS n 1 27 GLY n 1 28 PRO n 1 29 ARG n 1 30 LYS n 1 31 ARG n 1 32 LYS n 1 33 ALA n 1 34 ASP n 1 35 ALA n 1 36 SER 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 'Biological sequence' _entity_src_gen.pdbx_beg_seq_num 1 _entity_src_gen.pdbx_end_seq_num 36 _entity_src_gen.gene_src_common_name ? _entity_src_gen.gene_src_genus ? _entity_src_gen.pdbx_gene_src_gene 'cleD, CCNA_03198' _entity_src_gen.gene_src_species ? _entity_src_gen.gene_src_strain 'NA1000 / CB15N' _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 'Caulobacter vibrioides (strain NA1000 / CB15N)' _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 565050 _entity_src_gen.pdbx_gene_src_variant ? _entity_src_gen.pdbx_gene_src_cell_line ? _entity_src_gen.pdbx_gene_src_atcc 19089 _entity_src_gen.pdbx_gene_src_organ ? _entity_src_gen.pdbx_gene_src_organelle ? _entity_src_gen.pdbx_gene_src_cell ? _entity_src_gen.pdbx_gene_src_cellular_location ? _entity_src_gen.host_org_common_name ? _entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli BL21(DE3)' _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 469008 _entity_src_gen.host_org_genus ? _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 Plasmid _entity_src_gen.pdbx_host_org_vector pET28a _entity_src_gen.host_org_details pET28a-His-SUMO-ARR_CleD _entity_src_gen.expression_system_id ? _entity_src_gen.plasmid_name ? _entity_src_gen.plasmid_details ? _entity_src_gen.pdbx_description ? # _struct_ref.id 1 _struct_ref.db_name UNP _struct_ref.db_code A0A0H3CCM2_CAUVN _struct_ref.pdbx_db_accession A0A0H3CCM2 _struct_ref.pdbx_db_isoform ? _struct_ref.entity_id 1 _struct_ref.pdbx_seq_one_letter_code KPREWVEAVAYVGPDRRRFNSADYKGPRKRKADAS _struct_ref.pdbx_align_begin 140 # _struct_ref_seq.align_id 1 _struct_ref_seq.ref_id 1 _struct_ref_seq.pdbx_PDB_id_code 6SFT _struct_ref_seq.pdbx_strand_id A _struct_ref_seq.seq_align_beg 2 _struct_ref_seq.pdbx_seq_align_beg_ins_code ? _struct_ref_seq.seq_align_end 36 _struct_ref_seq.pdbx_seq_align_end_ins_code ? _struct_ref_seq.pdbx_db_accession A0A0H3CCM2 _struct_ref_seq.db_align_beg 140 _struct_ref_seq.pdbx_db_align_beg_ins_code ? _struct_ref_seq.db_align_end 174 _struct_ref_seq.pdbx_db_align_end_ins_code ? _struct_ref_seq.pdbx_auth_seq_align_beg 140 _struct_ref_seq.pdbx_auth_seq_align_end 174 # _struct_ref_seq_dif.align_id 1 _struct_ref_seq_dif.pdbx_pdb_id_code 6SFT _struct_ref_seq_dif.mon_id SER _struct_ref_seq_dif.pdbx_pdb_strand_id A _struct_ref_seq_dif.seq_num 1 _struct_ref_seq_dif.pdbx_pdb_ins_code ? _struct_ref_seq_dif.pdbx_seq_db_name UNP _struct_ref_seq_dif.pdbx_seq_db_accession_code A0A0H3CCM2 _struct_ref_seq_dif.db_mon_id ? _struct_ref_seq_dif.pdbx_seq_db_seq_num ? _struct_ref_seq_dif.details 'expression tag' _struct_ref_seq_dif.pdbx_auth_seq_num 139 _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 C2E non-polymer . ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; 'c-di-GMP; Cyclic diguanosine monophosphate' 'C20 H24 N10 O14 P2' 690.411 GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129 GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067 LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195 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 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 # loop_ _pdbx_nmr_exptl.experiment_id _pdbx_nmr_exptl.conditions_id _pdbx_nmr_exptl.solution_id _pdbx_nmr_exptl.type _pdbx_nmr_exptl.spectrometer_id _pdbx_nmr_exptl.sample_state 1 1 1 '2D 1H-15N HSQC' 1 isotropic 2 1 1 '2D 1H-15N HSQC' 2 isotropic 3 1 1 '3D 1H-15N NOESY' 1 isotropic 4 1 1 '3D 1H-15N TOCSY' 1 isotropic 5 1 1 '3D 1H-15N NH2 NOESY' 1 isotropic 9 1 1 '3D 1H-15N NH2 TOCSY' 1 isotropic 6 1 1 '2D 1H-1H NOESY' 2 isotropic 8 1 2 '3D HNCA' 3 isotropic 7 1 2 '3D HNCO' 3 isotropic 13 1 2 '3D CBCA(CO)NH' 3 isotropic 12 1 2 '3D HBHA(CO)NH' 3 isotropic 11 1 2 '3D CBCANH' 3 isotropic 10 1 2 '3D C(CO)NH' 1 isotropic 15 1 2 '2D 1H-1H NOESY isotpe filtered' 2 isotropic 16 1 1 '3D 15N t1 interleaved' 1 isotropic 14 1 1 '3D 15N t2 interleaved' 1 isotropic 17 1 1 '2D 1H-15N NOE without sturation' 1 isotropic 19 1 1 '2D 1H-15N NOE with sturation' 1 isotropic 24 1 2 '3D HN(CO)CA' 1 isotropic 18 2 2 '3D HN(CO)CA without decoupling' 1 anisotropic 25 1 2 '2D 1H-15N HSQC IPAP' 1 isotropic 23 2 2 '2D 1H-15N HSQC IPAP' 1 anisotropic # loop_ _pdbx_nmr_exptl_sample_conditions.conditions_id _pdbx_nmr_exptl_sample_conditions.temperature _pdbx_nmr_exptl_sample_conditions.pressure_units _pdbx_nmr_exptl_sample_conditions.pressure _pdbx_nmr_exptl_sample_conditions.pH _pdbx_nmr_exptl_sample_conditions.ionic_strength _pdbx_nmr_exptl_sample_conditions.details _pdbx_nmr_exptl_sample_conditions.ionic_strength_err _pdbx_nmr_exptl_sample_conditions.ionic_strength_units _pdbx_nmr_exptl_sample_conditions.label _pdbx_nmr_exptl_sample_conditions.pH_err _pdbx_nmr_exptl_sample_conditions.pH_units _pdbx_nmr_exptl_sample_conditions.pressure_err _pdbx_nmr_exptl_sample_conditions.temperature_err _pdbx_nmr_exptl_sample_conditions.temperature_units 1 298 atm 1 6.5 0.47 ? ? M conditions_1 0.04 pH ? 0.1 K 2 298 atm 1 6.5 0.31 ? ? M conditions_2 ? pH ? ? K # loop_ _pdbx_nmr_sample_details.solution_id _pdbx_nmr_sample_details.contents _pdbx_nmr_sample_details.solvent_system _pdbx_nmr_sample_details.label _pdbx_nmr_sample_details.type _pdbx_nmr_sample_details.details 1 ;1.0 mM [U-99% 15N] ARR_CleD, 3.0 mM C2E, 100 mM sodium chloride, 2 mM magnesim chloride, 20 mM sodium phosphate, 0.02 % sodium azide, 95% H2O/5% D2O ; '95% H2O/5% D2O' 15N_sample solution ? 2 ;0.9 mM [U-99% 13C; U-99% 15N] ARR_CleD, 2.7 mM C2E, 100 mM sodium chloride, 2 mM magnesium chloride, 20 mM sodium phosphate, 0.02 % sodium azide, 95% H2O/5% D2O ; '95% H2O/5% D2O' 15N_13C_sample solution ? 3 ;0.6 mM [U-99% 13C; U-99% 15N] ARR_CleD, 1.8 mM C2E, 66.6 mM sodium chloride, 1.33 mM magnesium chloride, 13.33 mM sodium phosphate, 9 mg/mL Pf1 phage, 90% H2O/10% D2O ; '90% H2O/10% D2O' 15N-13C-phages 'filamentous virus' 'D2O splitting of 8Hz is enough' # loop_ _pdbx_nmr_spectrometer.spectrometer_id _pdbx_nmr_spectrometer.model _pdbx_nmr_spectrometer.type _pdbx_nmr_spectrometer.manufacturer _pdbx_nmr_spectrometer.field_strength _pdbx_nmr_spectrometer.details 1 DRX ? Bruker 600 'TXI probe head' 2 DRX ? Bruker 900 'TCI probe head' 3 DRX ? Bruker 800 'TXI probe head' # _pdbx_nmr_refine.entry_id 6SFT _pdbx_nmr_refine.method 'simulated annealing' _pdbx_nmr_refine.details ? _pdbx_nmr_refine.software_ordinal 1 # _pdbx_nmr_ensemble.entry_id 6SFT _pdbx_nmr_ensemble.conformers_calculated_total_number 200 _pdbx_nmr_ensemble.conformers_submitted_total_number 10 _pdbx_nmr_ensemble.conformer_selection_criteria 'structures with the lowest energy' _pdbx_nmr_ensemble.representative_conformer ? _pdbx_nmr_ensemble.average_constraints_per_residue ? _pdbx_nmr_ensemble.average_constraint_violations_per_residue ? _pdbx_nmr_ensemble.maximum_distance_constraint_violation ? _pdbx_nmr_ensemble.average_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_upper_distance_constraint_violation ? _pdbx_nmr_ensemble.maximum_lower_distance_constraint_violation ? _pdbx_nmr_ensemble.distance_constraint_violation_method ? _pdbx_nmr_ensemble.maximum_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.average_torsion_angle_constraint_violation ? _pdbx_nmr_ensemble.torsion_angle_constraint_violation_method ? # _pdbx_nmr_representative.entry_id 6SFT _pdbx_nmr_representative.conformer_id 1 _pdbx_nmr_representative.selection_criteria 'lowest energy' # loop_ _pdbx_nmr_software.ordinal _pdbx_nmr_software.classification _pdbx_nmr_software.name _pdbx_nmr_software.version _pdbx_nmr_software.authors 1 refinement 'X-PLOR NIH' 2.34 'Schwieters, Kuszewski, Tjandra and Clore' 2 'structure calculation' 'X-PLOR NIH' 2.34 'Schwieters, Kuszewski, Tjandra and Clore' 3 'chemical shift assignment' Sparky 3.115 Goddard 4 'peak picking' Sparky 3.115 Goddard 5 processing NMRPipe 8.9 'Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax' 6 'data analysis' ModelFree 4 Palmer 7 'peak picking' PIPP ? Garrett 8 collection TopSpin ? 'Bruker Biospin' # _exptl.absorpt_coefficient_mu ? _exptl.absorpt_correction_T_max ? _exptl.absorpt_correction_T_min ? _exptl.absorpt_correction_type ? _exptl.absorpt_process_details ? _exptl.entry_id 6SFT _exptl.crystals_number ? _exptl.details ? _exptl.method 'SOLUTION NMR' _exptl.method_details ? # _struct.entry_id 6SFT _struct.title 'Solution structure of protein ARR_CleD in complex with c-di-GMP' _struct.pdbx_model_details ? _struct.pdbx_formula_weight ? _struct.pdbx_formula_weight_method ? _struct.pdbx_model_type_details ? _struct.pdbx_CASP_flag N # _struct_keywords.entry_id 6SFT _struct_keywords.text 'c-di-GMP, CleD, CheY, Response Regulator, Signaling protein' _struct_keywords.pdbx_keywords 'SIGNALING PROTEIN' # loop_ _struct_asym.id _struct_asym.pdbx_blank_PDB_chainid_flag _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N N 1 ? B N N 2 ? C N N 2 ? # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id ARG _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 31 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id ALA _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 35 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id ARG _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 169 _struct_conf.end_auth_comp_id ALA _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 173 _struct_conf.pdbx_PDB_helix_class 5 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 5 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? # _struct_sheet.id AA1 _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id AA1 _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense 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 AA1 1 VAL A 7 ? GLU A 8 ? VAL A 145 GLU A 146 AA1 2 VAL A 13 ? GLY A 14 ? VAL A 151 GLY A 152 # _pdbx_struct_sheet_hbond.sheet_id AA1 _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id VAL _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 7 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id VAL _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 145 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id GLY _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 14 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id GLY _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 152 # loop_ _struct_site.id _struct_site.pdbx_evidence_code _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id _struct_site.pdbx_auth_ins_code _struct_site.pdbx_num_residues _struct_site.details AC1 Software A C2E 501 ? 8 'binding site for residue C2E A 501' AC2 Software A C2E 502 ? 7 'binding site for residue C2E A 502' # 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 8 TYR A 12 ? TYR A 150 . ? 1_555 ? 2 AC1 8 ASP A 16 ? ASP A 154 . ? 1_555 ? 3 AC1 8 ARG A 17 ? ARG A 155 . ? 1_555 ? 4 AC1 8 ARG A 18 ? ARG A 156 . ? 1_555 ? 5 AC1 8 LYS A 30 ? LYS A 168 . ? 1_555 ? 6 AC1 8 ARG A 31 ? ARG A 169 . ? 1_555 ? 7 AC1 8 LYS A 32 ? LYS A 170 . ? 1_555 ? 8 AC1 8 C2E C . ? C2E A 502 . ? 1_555 ? 9 AC2 7 ARG A 17 ? ARG A 155 . ? 1_555 ? 10 AC2 7 ARG A 18 ? ARG A 156 . ? 1_555 ? 11 AC2 7 PHE A 20 ? PHE A 158 . ? 1_555 ? 12 AC2 7 TYR A 25 ? TYR A 163 . ? 1_555 ? 13 AC2 7 LYS A 30 ? LYS A 168 . ? 1_555 ? 14 AC2 7 ARG A 31 ? ARG A 169 . ? 1_555 ? 15 AC2 7 C2E B . ? C2E A 501 . ? 1_555 ? # _atom_sites.entry_id 6SFT _atom_sites.Cartn_transf_matrix[1][1] ? _atom_sites.Cartn_transf_matrix[1][2] ? _atom_sites.Cartn_transf_matrix[1][3] ? _atom_sites.Cartn_transf_matrix[2][1] ? _atom_sites.Cartn_transf_matrix[2][2] ? _atom_sites.Cartn_transf_matrix[2][3] ? _atom_sites.Cartn_transf_matrix[3][1] ? _atom_sites.Cartn_transf_matrix[3][2] ? _atom_sites.Cartn_transf_matrix[3][3] ? _atom_sites.Cartn_transf_vector[1] ? _atom_sites.Cartn_transf_vector[2] ? _atom_sites.Cartn_transf_vector[3] ? _atom_sites.fract_transf_matrix[1][1] 1.000000 _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] 1.000000 _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] 1.000000 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 _atom_sites.solution_primary ? _atom_sites.solution_secondary ? _atom_sites.solution_hydrogens ? _atom_sites.special_details ? # loop_ _atom_type.symbol C H N O P # 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 SER 1 139 139 SER SER A . n A 1 2 LYS 2 140 140 LYS LYS A . n A 1 3 PRO 3 141 141 PRO PRO A . n A 1 4 ARG 4 142 142 ARG ARG A . n A 1 5 GLU 5 143 143 GLU GLU A . n A 1 6 TRP 6 144 144 TRP TRP A . n A 1 7 VAL 7 145 145 VAL VAL A . n A 1 8 GLU 8 146 146 GLU GLU A . n A 1 9 ALA 9 147 147 ALA ALA A . n A 1 10 VAL 10 148 148 VAL VAL A . n A 1 11 ALA 11 149 149 ALA ALA A . n A 1 12 TYR 12 150 150 TYR TYR A . n A 1 13 VAL 13 151 151 VAL VAL A . n A 1 14 GLY 14 152 152 GLY GLY A . n A 1 15 PRO 15 153 153 PRO PRO A . n A 1 16 ASP 16 154 154 ASP ASP A . n A 1 17 ARG 17 155 155 ARG ARG A . n A 1 18 ARG 18 156 156 ARG ARG A . n A 1 19 ARG 19 157 157 ARG ARG A . n A 1 20 PHE 20 158 158 PHE PHE A . n A 1 21 ASN 21 159 159 ASN ASN A . n A 1 22 SER 22 160 160 SER SER A . n A 1 23 ALA 23 161 161 ALA ALA A . n A 1 24 ASP 24 162 162 ASP ASP A . n A 1 25 TYR 25 163 163 TYR TYR A . n A 1 26 LYS 26 164 164 LYS LYS A . n A 1 27 GLY 27 165 165 GLY GLY A . n A 1 28 PRO 28 166 166 PRO PRO A . n A 1 29 ARG 29 167 167 ARG ARG A . n A 1 30 LYS 30 168 168 LYS LYS A . n A 1 31 ARG 31 169 169 ARG ARG A . n A 1 32 LYS 32 170 170 LYS LYS A . n A 1 33 ALA 33 171 171 ALA ALA A . n A 1 34 ASP 34 172 172 ASP ASP A . n A 1 35 ALA 35 173 173 ALA ALA A . n A 1 36 SER 36 174 174 SER SER 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 C2E 1 501 501 C2E C2E A . C 2 C2E 1 502 502 C2E C2E 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 # 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)' 2010 ? 1 MORE 9 ? 1 'SSA (A^2)' 4020 ? # _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 ? _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 2020-06-10 2 'Structure model' 1 1 2021-01-13 3 'Structure model' 1 2 2023-06-14 # _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' 'Database references' 2 3 'Structure model' 'Database references' 3 3 '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 2 'Structure model' citation 2 2 'Structure model' citation_author 3 3 'Structure model' database_2 4 3 'Structure model' pdbx_database_status # 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 2 'Structure model' '_citation.country' 2 2 'Structure model' '_citation.journal_abbrev' 3 2 'Structure model' '_citation.journal_id_ASTM' 4 2 'Structure model' '_citation.journal_id_CSD' 5 2 'Structure model' '_citation.journal_id_ISSN' 6 2 'Structure model' '_citation.journal_volume' 7 2 'Structure model' '_citation.page_first' 8 2 'Structure model' '_citation.page_last' 9 2 'Structure model' '_citation.pdbx_database_id_DOI' 10 2 'Structure model' '_citation.pdbx_database_id_PubMed' 11 2 'Structure model' '_citation.title' 12 2 'Structure model' '_citation.year' 13 3 'Structure model' '_database_2.pdbx_DOI' 14 3 'Structure model' '_database_2.pdbx_database_accession' 15 3 'Structure model' '_pdbx_database_status.status_code_nmr_data' # _pdbx_entry_details.entry_id 6SFT _pdbx_entry_details.nonpolymer_details ? _pdbx_entry_details.sequence_details ? _pdbx_entry_details.compound_details ? _pdbx_entry_details.source_details ? _pdbx_entry_details.has_ligand_of_interest Y # loop_ _pdbx_nmr_exptl_sample.solution_id _pdbx_nmr_exptl_sample.component _pdbx_nmr_exptl_sample.concentration _pdbx_nmr_exptl_sample.concentration_range _pdbx_nmr_exptl_sample.concentration_units _pdbx_nmr_exptl_sample.isotopic_labeling 1 ARR_CleD 1.0 ? mM '[U-99% 15N]' 1 C2E 3.0 ? mM 'natural abundance' 1 'sodium chloride' 100 ? mM 'natural abundance' 1 'magnesim chloride' 2 ? mM 'natural abundance' 1 'sodium phosphate' 20 ? mM 'natural abundance' 1 'sodium azide' 0.02 ? % 'natural abundance' 2 ARR_CleD 0.9 ? mM '[U-99% 13C; U-99% 15N]' 2 C2E 2.7 ? mM 'natural abundance' 2 'sodium chloride' 100 ? mM 'natural abundance' 2 'magnesium chloride' 2 ? mM 'natural abundance' 2 'sodium phosphate' 20 ? mM 'natural abundance' 2 'sodium azide' 0.02 ? % 'natural abundance' 3 ARR_CleD 0.6 ? mM '[U-99% 13C; U-99% 15N]' 3 C2E 1.8 ? mM 'natural abundance' 3 'sodium chloride' 66.6 ? mM 'natural abundance' 3 'magnesium chloride' 1.33 ? mM 'natural abundance' 3 'sodium phosphate' 13.33 ? mM 'natural abundance' 3 'Pf1 phage' 9 ? mg/mL 'natural abundance' # 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 LYS A 140 ? ? -161.71 75.14 2 1 ARG A 142 ? ? -70.55 -136.04 3 1 ARG A 157 ? ? -155.41 -13.03 4 1 LYS A 168 ? ? -144.12 14.55 5 2 PRO A 141 ? ? -78.64 -124.73 6 2 ARG A 142 ? ? -146.87 47.60 7 2 ARG A 157 ? ? -155.61 -10.45 8 2 LYS A 168 ? ? -143.86 15.12 9 3 LYS A 140 ? ? -165.24 59.62 10 3 ARG A 142 ? ? -69.73 -138.84 11 3 GLU A 143 ? ? 53.24 72.51 12 3 ARG A 157 ? ? -155.74 -7.57 13 3 LYS A 168 ? ? -141.24 14.63 14 4 LYS A 140 ? ? -165.39 67.00 15 4 PRO A 141 ? ? -81.73 -121.19 16 4 ARG A 157 ? ? -155.95 -9.53 17 4 LYS A 168 ? ? -141.08 14.24 18 5 LYS A 140 ? ? 53.64 76.82 19 5 PRO A 141 ? ? -55.31 171.80 20 5 ARG A 157 ? ? -150.36 -11.91 21 5 LYS A 168 ? ? -143.02 15.35 22 6 ARG A 142 ? ? -72.69 -134.89 23 6 ARG A 157 ? ? -155.80 -9.84 24 7 ARG A 142 ? ? -66.25 -137.62 25 7 ARG A 157 ? ? -154.99 -14.90 26 7 LYS A 168 ? ? -145.13 16.91 27 8 LYS A 140 ? ? -163.34 -42.75 28 8 PRO A 141 ? ? -94.75 -112.37 29 8 ARG A 142 ? ? -135.48 -130.83 30 8 LYS A 168 ? ? -141.58 14.20 31 9 ARG A 142 ? ? -65.83 -132.17 32 9 ARG A 157 ? ? -155.95 -8.69 33 9 LYS A 168 ? ? -142.69 15.00 34 10 ARG A 142 ? ? -71.45 -136.00 35 10 ARG A 157 ? ? -155.53 -11.41 36 10 LYS A 168 ? ? -144.27 15.40 # _pdbx_audit_support.funding_organization 'Swiss National Science Foundation' _pdbx_audit_support.country Switzerland _pdbx_audit_support.grant_number 'SNF 31-149927' _pdbx_audit_support.ordinal 1 # _pdbx_entity_instance_feature.ordinal 1 _pdbx_entity_instance_feature.comp_id C2E _pdbx_entity_instance_feature.asym_id ? _pdbx_entity_instance_feature.seq_num ? _pdbx_entity_instance_feature.auth_comp_id C2E _pdbx_entity_instance_feature.auth_asym_id ? _pdbx_entity_instance_feature.auth_seq_num ? _pdbx_entity_instance_feature.feature_type 'SUBJECT OF INVESTIGATION' _pdbx_entity_instance_feature.details ? # _pdbx_entity_nonpoly.entity_id 2 _pdbx_entity_nonpoly.name ;9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one) ; _pdbx_entity_nonpoly.comp_id C2E # _pdbx_struct_assembly_auth_evidence.id 1 _pdbx_struct_assembly_auth_evidence.assembly_id 1 _pdbx_struct_assembly_auth_evidence.experimental_support 'isothermal titration calorimetry' _pdbx_struct_assembly_auth_evidence.details 'dissociation constant K_D - 110 nM' #