data_wwPDB_remediated_restraints_file_for_PDB_entry_1nyb # This wwPDB archive file contains, for PDB entry 1nyb: # # - 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_1nyb _Entry.Title "wwPDB remediated NMR restraints for PDB entry 1nyb" _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 1nyb" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_1nyb _Assembly.ID 1 _Assembly.Name 1nyb _Assembly.Number_of_components 2 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state "not present" _Assembly.Molecular_mass 10306.59764 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 "BoxB RNA" 1 $BoxB_RNA A . no . . . . . . rr_1nyb 1 2 "Probable regulatory protein N" 2 $Probable_regulatory_protein_N B . no . . . . . . rr_1nyb 1 stop_ save_ save_BoxB_RNA _Entity.Sf_category entity _Entity.Sf_framecode BoxB_RNA _Entity.Entry_ID rr_1nyb _Entity.ID 1 _Entity.Name BoxB_RNA _Entity.Type polymer _Entity.Polymer_type polyribonucleotide _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code ; GGUUCACCUCUAACCGGGUG AGCC ; _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 24 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 7724.62094 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 . G . rr_1nyb 1 2 . G . rr_1nyb 1 3 . U . rr_1nyb 1 4 . U . rr_1nyb 1 5 . C . rr_1nyb 1 6 . A . rr_1nyb 1 7 . C . rr_1nyb 1 8 . C . rr_1nyb 1 9 . U . rr_1nyb 1 10 . C . rr_1nyb 1 11 . U . rr_1nyb 1 12 . A . rr_1nyb 1 13 . A . rr_1nyb 1 14 . C . rr_1nyb 1 15 . C . rr_1nyb 1 16 . G . rr_1nyb 1 17 . G . rr_1nyb 1 18 . G . rr_1nyb 1 19 . U . rr_1nyb 1 20 . G . rr_1nyb 1 21 . A . rr_1nyb 1 22 . G . rr_1nyb 1 23 . C . rr_1nyb 1 24 . C . rr_1nyb 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 . G 1 1 rr_1nyb 1 . G 2 2 rr_1nyb 1 . U 3 3 rr_1nyb 1 . U 4 4 rr_1nyb 1 . C 5 5 rr_1nyb 1 . A 6 6 rr_1nyb 1 . C 7 7 rr_1nyb 1 . C 8 8 rr_1nyb 1 . U 9 9 rr_1nyb 1 . C 10 10 rr_1nyb 1 . U 11 11 rr_1nyb 1 . A 12 12 rr_1nyb 1 . A 13 13 rr_1nyb 1 . C 14 14 rr_1nyb 1 . C 15 15 rr_1nyb 1 . G 16 16 rr_1nyb 1 . G 17 17 rr_1nyb 1 . G 18 18 rr_1nyb 1 . U 19 19 rr_1nyb 1 . G 20 20 rr_1nyb 1 . A 21 21 rr_1nyb 1 . G 22 22 rr_1nyb 1 . C 23 23 rr_1nyb 1 . C 24 24 rr_1nyb 1 stop_ save_ save_Probable_regulatory_protein_N _Entity.Sf_category entity _Entity.Sf_framecode Probable_regulatory_protein_N _Entity.Entry_ID rr_1nyb _Entity.ID 2 _Entity.Name Probable_regulatory_protein_N _Entity.Type polymer _Entity.Polymer_type polypeptide(L) _Entity.Polymer_strand_ID B _Entity.Polymer_seq_one_letter_code ; ESKGTAKSRYKARRAELIAE RR ; _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 22 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 2 _Entity.Formula_weight 2581.9767 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 . GLU . rr_1nyb 2 2 . SER . rr_1nyb 2 3 . LYS . rr_1nyb 2 4 . GLY . rr_1nyb 2 5 . THR . rr_1nyb 2 6 . ALA . rr_1nyb 2 7 . LYS . rr_1nyb 2 8 . SER . rr_1nyb 2 9 . ARG . rr_1nyb 2 10 . TYR . rr_1nyb 2 11 . LYS . rr_1nyb 2 12 . ALA . rr_1nyb 2 13 . ARG . rr_1nyb 2 14 . ARG . rr_1nyb 2 15 . ALA . rr_1nyb 2 16 . GLU . rr_1nyb 2 17 . LEU . rr_1nyb 2 18 . ILE . rr_1nyb 2 19 . ALA . rr_1nyb 2 20 . GLU . rr_1nyb 2 21 . ARG . rr_1nyb 2 22 . ARG . rr_1nyb 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 . GLU 1 1 rr_1nyb 2 . SER 2 2 rr_1nyb 2 . LYS 3 3 rr_1nyb 2 . GLY 4 4 rr_1nyb 2 . THR 5 5 rr_1nyb 2 . ALA 6 6 rr_1nyb 2 . LYS 7 7 rr_1nyb 2 . SER 8 8 rr_1nyb 2 . ARG 9 9 rr_1nyb 2 . TYR 10 10 rr_1nyb 2 . LYS 11 11 rr_1nyb 2 . ALA 12 12 rr_1nyb 2 . ARG 13 13 rr_1nyb 2 . ARG 14 14 rr_1nyb 2 . ALA 15 15 rr_1nyb 2 . GLU 16 16 rr_1nyb 2 . LEU 17 17 rr_1nyb 2 . ILE 18 18 rr_1nyb 2 . ALA 19 19 rr_1nyb 2 . GLU 20 20 rr_1nyb 2 . ARG 21 21 rr_1nyb 2 . ARG 22 22 rr_1nyb 2 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_1nyb _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 15 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_1nyb _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 1nyb.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_1nyb 1 1 1nyb.mr . . unknown 2 distance NOE simple 0 rr_1nyb 1 1 1nyb.mr . . unknown 3 "dihedral angle" "Not applicable" "Not applicable" 0 rr_1nyb 1 1 1nyb.mr . . unknown 4 distance NOE simple 0 rr_1nyb 1 1 1nyb.mr . . unknown 5 distance "hydrogen bond" simple 0 rr_1nyb 1 1 1nyb.mr . . unknown 6 "dihedral angle" "Not applicable" "Not applicable" 0 rr_1nyb 1 1 1nyb.mr . . unknown 7 distance NOE simple 0 rr_1nyb 1 1 1nyb.mr . . "MR format" 8 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_1nyb 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_1nyb _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 TRANSCRIPTION/RNA 12-FEB-03 1NYB *TITLE SOLUTION STRUCTURE OF THE BACTERIOPHAGE PHI21 N PEPTIDE- *TITLE 2 BOXB RNA COMPLEX *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: PROBABLE REGULATORY PROTEIN N; *COMPND 3 CHAIN: A; *COMPND 4 ENGINEERED: YES; *COMPND 5 MOL_ID: 2; *COMPND 6 MOLECULE: BOXB RNA; *COMPND 7 CHAIN: B; *COMPND 8 ENGINEERED: YES *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE PHI-21; *SOURCE 3 ORGANISM_COMMON: VIRUS; *SOURCE 4 GENE: N; *SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; *SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; *SOURCE 7 MOL_ID: 2; *SOURCE 8 SYNTHETIC: YES; *SOURCE 9 OTHER_DETAILS: SYNTHESIS OF THE RNA FRAGMENT FROM THE *SOURCE 10 BACTERIOPHAGE PHI21 BOXB *KEYWDS PEPTIDE-RNA COMPLEX, TRANSCRIPTION ANTITERMINATION *EXPDTA NMR, 15 STRUCTURES *AUTHOR C.D.CILLEY, J.R.WILLIAMSON *REVDAT 1 24-JUN-03 1NYB 0 ; save_