data_wwPDB_remediated_restraints_file_for_PDB_entry_2o9l # This wwPDB archive file contains, for PDB entry 2o9l: # # - Sequence information from the PDB mmCIF file # - NMR restraints from the PDB MR file # # In this file, the NMR restraints share the same atom names as in the coordinate # file, and in this way can differ from the data deposited at the wwPDB. To achieve # this aim, the NMR restraints were parsed from their original format files, and # the coordinates and NMR restraints information were subsequently harmonized. # # Due to the complexity of this harmonization process, minor modifications could # have occurred to the NMR restraints information, or data could have been lost # because of parsing or conversion errors. The PDB file remains the # authoritative reference for the atomic coordinates and the originally deposited # restraints files remain the primary reference for these data. # # This file is generated as part of the wwPDB at the BioMagResBank (BMRB) in # collaboration with the PDBe (formerly MSD) group at the European # Bioinformatics Institute (EBI) and the CMBI/IMM group at the Radboud # University of Nijmegen. # # Several software packages were used to produce this file: # # - Wattos (BMRB and CMBI/IMM). # - FormatConverter and NMRStarExport (PDBe). # - CCPN framework (http://www.ccpn.ac.uk/). # # More information about this process can be found in the references below. # Please cite the original reference for this PDB entry. # # JF Doreleijers, A Nederveen, W Vranken, J Lin, AM Bonvin, R Kaptein, JL # Markley, and EL Ulrich (2005). BioMagResBank databases DOCR and FRED # containing converted and filtered sets of experimental NMR restraints and # coordinates from over 500 protein PDB structures. J. Biomol. NMR 32, 1-12. # # WF Vranken, W Boucher, TJ Stevens, RH Fogh, A Pajon, M Llinas, EL Ulrich, JL # Markley, J Ionides, ED Laue (2005). The CCPN data model for NMR spectroscopy: # development of a software pipeline. Proteins 59, 687-696. # # JF Doreleijers, WF Vranken, C Schulte, J Lin, JR Wedell, CJ Penkett, GW Vuister, # G Vriend, JL Markley, and EL Ulrich (2009). The NMR Restraints Grid at BMRB for # 5,266 Protein and Nucleic Acid PDB Entries. J Biomol. NMR 45, 389–396. save_entry_information _Entry.Sf_category entry_information _Entry.Sf_framecode entry_information _Entry.ID rr_2o9l _Entry.Title "wwPDB remediated NMR restraints for PDB entry 2o9l" _Entry.NMR_STAR_version 3.1 _Entry.Experimental_method NMR _Entry.Experimental_method_subtype solution _Entry.Details "Contains the remediated restraint lists and coordinates for PDB entry 2o9l" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_2o9l _Assembly.ID 1 _Assembly.Name 2o9l _Assembly.Number_of_components 3 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state "not present" _Assembly.Molecular_mass 16141.22638 loop_ _Entity_assembly.ID _Entity_assembly.Entity_assembly_name _Entity_assembly.Entity_ID _Entity_assembly.Entity_label _Entity_assembly.Asym_ID _Entity_assembly.PDB_chain_ID _Entity_assembly.Experimental_data_reported _Entity_assembly.Physical_state _Entity_assembly.Conformational_isomer _Entity_assembly.Chemical_exchange_state _Entity_assembly.Magnetic_equivalence_group_code _Entity_assembly.Role _Entity_assembly.Details _Entity_assembly.Entry_ID _Entity_assembly.Assembly_ID 1 "5 D TP TP TP TP GP GP CP AP CP GP TP TP TP C 3" 1 $5__D__TP_TP_TP_TP_GP_GP_CP_AP_CP_GP_TP_TP_TP_C__3_ A . no . . . . . . rr_2o9l 1 2 "5 D GP AP AP AP CP GP TP GP CP CP AP AP AP A 3" 3 $5__D__GP_AP_AP_AP_CP_GP_TP_GP_CP_CP_AP_AP_AP_A__3_ B . no . . . . . . rr_2o9l 1 3 "RNA polymerase sigma factor RpoN" 2 $RNA_polymerase_sigma_factor_RpoN C . no . . . . . . rr_2o9l 1 stop_ save_ save_5__D__TP_TP_TP_TP_GP_GP_CP_AP_CP_GP_TP_TP_TP_C__3_ _Entity.Sf_category entity _Entity.Sf_framecode 5__D__TP_TP_TP_TP_GP_GP_CP_AP_CP_GP_TP_TP_TP_C__3_ _Entity.Entry_ID rr_2o9l _Entity.ID 1 _Entity.Name 5__D__TP_TP_TP_TP_GP_GP_CP_AP_CP_GP_TP_TP_TP_C__3_ _Entity.Type polymer _Entity.Polymer_type polydeoxyribonucleotide _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code TTTTGGCACGTTTC _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality yes _Entity.Nstd_linkage no _Entity.Number_of_monomers 14 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 4304.68454 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . DT . rr_2o9l 1 2 . DT . rr_2o9l 1 3 . DT . rr_2o9l 1 4 . DT . rr_2o9l 1 5 . DG . rr_2o9l 1 6 . DG . rr_2o9l 1 7 . DC . rr_2o9l 1 8 . DA . rr_2o9l 1 9 . DC . rr_2o9l 1 10 . DG . rr_2o9l 1 11 . DT . rr_2o9l 1 12 . DT . rr_2o9l 1 13 . DT . rr_2o9l 1 14 . DC . rr_2o9l 1 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . DT 1 1 rr_2o9l 1 . DT 2 2 rr_2o9l 1 . DT 3 3 rr_2o9l 1 . DT 4 4 rr_2o9l 1 . DG 5 5 rr_2o9l 1 . DG 6 6 rr_2o9l 1 . DC 7 7 rr_2o9l 1 . DA 8 8 rr_2o9l 1 . DC 9 9 rr_2o9l 1 . DG 10 10 rr_2o9l 1 . DT 11 11 rr_2o9l 1 . DT 12 12 rr_2o9l 1 . DT 13 13 rr_2o9l 1 . DC 14 14 rr_2o9l 1 stop_ save_ save_RNA_polymerase_sigma_factor_RpoN _Entity.Sf_category entity _Entity.Sf_framecode RNA_polymerase_sigma_factor_RpoN _Entity.Entry_ID rr_2o9l _Entity.ID 2 _Entity.Name RNA_polymerase_sigma_factor_RpoN _Entity.Type polymer _Entity.Polymer_type polypeptide(L) _Entity.Polymer_strand_ID C _Entity.Polymer_seq_one_letter_code ; HMLTQGELMKLIKEIVENED KRKPYSDQEIANILKEKGFK VARRTVAKYREMLGIPSSRE RRI ; _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality no _Entity.Nstd_linkage no _Entity.Number_of_monomers 63 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 2 _Entity.Formula_weight 7477.7769 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . HIS . rr_2o9l 2 2 . MET . rr_2o9l 2 3 . LEU . rr_2o9l 2 4 . THR . rr_2o9l 2 5 . GLN . rr_2o9l 2 6 . GLY . rr_2o9l 2 7 . GLU . rr_2o9l 2 8 . LEU . rr_2o9l 2 9 . MET . rr_2o9l 2 10 . LYS . rr_2o9l 2 11 . LEU . rr_2o9l 2 12 . ILE . rr_2o9l 2 13 . LYS . rr_2o9l 2 14 . GLU . rr_2o9l 2 15 . ILE . rr_2o9l 2 16 . VAL . rr_2o9l 2 17 . GLU . rr_2o9l 2 18 . ASN . rr_2o9l 2 19 . GLU . rr_2o9l 2 20 . ASP . rr_2o9l 2 21 . LYS . rr_2o9l 2 22 . ARG . rr_2o9l 2 23 . LYS . rr_2o9l 2 24 . PRO . rr_2o9l 2 25 . TYR . rr_2o9l 2 26 . SER . rr_2o9l 2 27 . ASP . rr_2o9l 2 28 . GLN . rr_2o9l 2 29 . GLU . rr_2o9l 2 30 . ILE . rr_2o9l 2 31 . ALA . rr_2o9l 2 32 . ASN . rr_2o9l 2 33 . ILE . rr_2o9l 2 34 . LEU . rr_2o9l 2 35 . LYS . rr_2o9l 2 36 . GLU . rr_2o9l 2 37 . LYS . rr_2o9l 2 38 . GLY . rr_2o9l 2 39 . PHE . rr_2o9l 2 40 . LYS . rr_2o9l 2 41 . VAL . rr_2o9l 2 42 . ALA . rr_2o9l 2 43 . ARG . rr_2o9l 2 44 . ARG . rr_2o9l 2 45 . THR . rr_2o9l 2 46 . VAL . rr_2o9l 2 47 . ALA . rr_2o9l 2 48 . LYS . rr_2o9l 2 49 . TYR . rr_2o9l 2 50 . ARG . rr_2o9l 2 51 . GLU . rr_2o9l 2 52 . MET . rr_2o9l 2 53 . LEU . rr_2o9l 2 54 . GLY . rr_2o9l 2 55 . ILE . rr_2o9l 2 56 . PRO . rr_2o9l 2 57 . SER . rr_2o9l 2 58 . SER . rr_2o9l 2 59 . ARG . rr_2o9l 2 60 . GLU . rr_2o9l 2 61 . ARG . rr_2o9l 2 62 . ARG . rr_2o9l 2 63 . ILE . rr_2o9l 2 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . HIS 1 1 rr_2o9l 2 . MET 2 2 rr_2o9l 2 . LEU 3 3 rr_2o9l 2 . THR 4 4 rr_2o9l 2 . GLN 5 5 rr_2o9l 2 . GLY 6 6 rr_2o9l 2 . GLU 7 7 rr_2o9l 2 . LEU 8 8 rr_2o9l 2 . MET 9 9 rr_2o9l 2 . LYS 10 10 rr_2o9l 2 . LEU 11 11 rr_2o9l 2 . ILE 12 12 rr_2o9l 2 . LYS 13 13 rr_2o9l 2 . GLU 14 14 rr_2o9l 2 . ILE 15 15 rr_2o9l 2 . VAL 16 16 rr_2o9l 2 . GLU 17 17 rr_2o9l 2 . ASN 18 18 rr_2o9l 2 . GLU 19 19 rr_2o9l 2 . ASP 20 20 rr_2o9l 2 . LYS 21 21 rr_2o9l 2 . ARG 22 22 rr_2o9l 2 . LYS 23 23 rr_2o9l 2 . PRO 24 24 rr_2o9l 2 . TYR 25 25 rr_2o9l 2 . SER 26 26 rr_2o9l 2 . ASP 27 27 rr_2o9l 2 . GLN 28 28 rr_2o9l 2 . GLU 29 29 rr_2o9l 2 . ILE 30 30 rr_2o9l 2 . ALA 31 31 rr_2o9l 2 . ASN 32 32 rr_2o9l 2 . ILE 33 33 rr_2o9l 2 . LEU 34 34 rr_2o9l 2 . LYS 35 35 rr_2o9l 2 . GLU 36 36 rr_2o9l 2 . LYS 37 37 rr_2o9l 2 . GLY 38 38 rr_2o9l 2 . PHE 39 39 rr_2o9l 2 . LYS 40 40 rr_2o9l 2 . VAL 41 41 rr_2o9l 2 . ALA 42 42 rr_2o9l 2 . ARG 43 43 rr_2o9l 2 . ARG 44 44 rr_2o9l 2 . THR 45 45 rr_2o9l 2 . VAL 46 46 rr_2o9l 2 . ALA 47 47 rr_2o9l 2 . LYS 48 48 rr_2o9l 2 . TYR 49 49 rr_2o9l 2 . ARG 50 50 rr_2o9l 2 . GLU 51 51 rr_2o9l 2 . MET 52 52 rr_2o9l 2 . LEU 53 53 rr_2o9l 2 . GLY 54 54 rr_2o9l 2 . ILE 55 55 rr_2o9l 2 . PRO 56 56 rr_2o9l 2 . SER 57 57 rr_2o9l 2 . SER 58 58 rr_2o9l 2 . ARG 59 59 rr_2o9l 2 . GLU 60 60 rr_2o9l 2 . ARG 61 61 rr_2o9l 2 . ARG 62 62 rr_2o9l 2 . ILE 63 63 rr_2o9l 2 stop_ save_ save_5__D__GP_AP_AP_AP_CP_GP_TP_GP_CP_CP_AP_AP_AP_A__3_ _Entity.Sf_category entity _Entity.Sf_framecode 5__D__GP_AP_AP_AP_CP_GP_TP_GP_CP_CP_AP_AP_AP_A__3_ _Entity.Entry_ID rr_2o9l _Entity.ID 3 _Entity.Name 5__D__GP_AP_AP_AP_CP_GP_TP_GP_CP_CP_AP_AP_AP_A__3_ _Entity.Type polymer _Entity.Polymer_type polydeoxyribonucleotide _Entity.Polymer_strand_ID B _Entity.Polymer_seq_one_letter_code GAAACGTGCCAAAA _Entity.Ambiguous_conformational_states no _Entity.Ambiguous_chem_comp_sites no _Entity.Nstd_monomer no _Entity.Nstd_chirality yes _Entity.Nstd_linkage no _Entity.Number_of_monomers 14 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 3 _Entity.Formula_weight 4358.76494 loop_ _Entity_comp_index.ID _Entity_comp_index.Auth_seq_ID _Entity_comp_index.Comp_ID _Entity_comp_index.Comp_label _Entity_comp_index.Entry_ID _Entity_comp_index.Entity_ID 1 . DG . rr_2o9l 3 2 . DA . rr_2o9l 3 3 . DA . rr_2o9l 3 4 . DA . rr_2o9l 3 5 . DC . rr_2o9l 3 6 . DG . rr_2o9l 3 7 . DT . rr_2o9l 3 8 . DG . rr_2o9l 3 9 . DC . rr_2o9l 3 10 . DC . rr_2o9l 3 11 . DA . rr_2o9l 3 12 . DA . rr_2o9l 3 13 . DA . rr_2o9l 3 14 . DA . rr_2o9l 3 stop_ loop_ _Entity_poly_seq.Hetero _Entity_poly_seq.Mon_ID _Entity_poly_seq.Num _Entity_poly_seq.Comp_index_ID _Entity_poly_seq.Entry_ID _Entity_poly_seq.Entity_ID . DG 1 1 rr_2o9l 3 . DA 2 2 rr_2o9l 3 . DA 3 3 rr_2o9l 3 . DA 4 4 rr_2o9l 3 . DC 5 5 rr_2o9l 3 . DG 6 6 rr_2o9l 3 . DT 7 7 rr_2o9l 3 . DG 8 8 rr_2o9l 3 . DC 9 9 rr_2o9l 3 . DC 10 10 rr_2o9l 3 . DA 11 11 rr_2o9l 3 . DA 12 12 rr_2o9l 3 . DA 13 13 rr_2o9l 3 . DA 14 14 rr_2o9l 3 stop_ save_ save_conformer_statistics _Conformer_stat_list.Sf_category conformer_statistics _Conformer_stat_list.Sf_framecode conformer_statistics _Conformer_stat_list.Entry_ID rr_2o9l _Conformer_stat_list.ID 1 _Conformer_stat_list.Conf_family_coord_set_ID 1 _Conformer_stat_list.Conf_family_coord_set_label $Original_constraints_and_structures _Conformer_stat_list.Conformer_submitted_total_num 19 save_ save_global_Org_file_characteristics _Constraint_stat_list.Sf_framecode global_Org_file_characteristics _Constraint_stat_list.Sf_category constraint_statistics _Constraint_stat_list.Entry_ID rr_2o9l _Constraint_stat_list.ID 1 loop_ _Constraint_file.ID _Constraint_file.Constraint_filename _Constraint_file.Software_ID _Constraint_file.Software_label _Constraint_file.Software_name _Constraint_file.Block_ID _Constraint_file.Constraint_type _Constraint_file.Constraint_subtype _Constraint_file.Constraint_subsubtype _Constraint_file.Constraint_number _Constraint_file.Entry_ID _Constraint_file.Constraint_stat_list_ID 1 2o9l.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_2o9l 1 1 2o9l.mr . . AMBER 2 distance NOE simple 0 rr_2o9l 1 1 2o9l.mr . . AMBER 3 "dihedral angle" "Not applicable" "Not applicable" 0 rr_2o9l 1 1 2o9l.mr . . "MR format" 4 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_2o9l 1 stop_ save_ save_MR_file_comment_1 _Org_constr_file_comment.Sf_framecode MR_file_comment_1 _Org_constr_file_comment.Sf_category org_constr_file_comment _Org_constr_file_comment.Entry_ID rr_2o9l _Org_constr_file_comment.ID 1 _Org_constr_file_comment.Constraint_file_ID 1 _Org_constr_file_comment.Block_ID 1 _Org_constr_file_comment.Details "Generated by Wattos" _Org_constr_file_comment.Comment ; *HEADER RNA POLYMERASE SIGMA FACTOR RPON/DNA 13-DEC-06 2O9L *TITLE AMBER REFINED NMR STRUCTURE OF THE SIGMA-54 RPON DOMAIN *TITLE 2 BOUND TO THE-24 PROMOTER ELEMENT *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: RNA POLYMERASE SIGMA FACTOR RPON; *COMPND 3 CHAIN: A; *COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; *COMPND 5 ENGINEERED: YES; *COMPND 6 MOL_ID: 2; *COMPND 7 MOLECULE: 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)- *COMPND 8 3'; *COMPND 9 CHAIN: B; *COMPND 10 ENGINEERED: YES; *COMPND 11 OTHER_DETAILS: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE *COMPND 12 STRAND; *COMPND 13 MOL_ID: 3; *COMPND 14 MOLECULE: 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)- *COMPND 15 3'; *COMPND 16 CHAIN: C; *COMPND 17 ENGINEERED: YES; *COMPND 18 OTHER_DETAILS: NIRB SIGMA-54 BINDING SITE NON-TEMPLATE *COMPND 19 STRAND *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; *SOURCE 3 ORGANISM_COMMON: BACTERIA; *SOURCE 4 GENE: RPON; *SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; *SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; *SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) WITH ROSETTA.PLYSS; *SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; *SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSKB3; *SOURCE 10 MOL_ID: 2; *SOURCE 11 SYNTHETIC: YES; *SOURCE 12 MOL_ID: 3; *SOURCE 13 SYNTHETIC: YES *KEYWDS AMBER, GENERALIZED BORN SOLVENT MODEL, PROTEIN-DNA COMPLEX, *KEYWDS 2 HELIX-TURN-HELIX, TRANSCRIPTION FACTOR, SIGMA-54, RNA *KEYWDS 3 POLYMERASE *EXPDTA NMR, 19 STRUCTURES *AUTHOR M.DOUCLEFF, J.G.PELTON, P.S.LEE, D.E.WEMMER *REVDAT 1 17-JUL-07 2O9L 0 ; save_