data_wwPDB_remediated_restraints_file_for_PDB_entry_1pjf # This wwPDB archive file contains, for PDB entry 1pjf: # # - 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_1pjf _Entry.Title "wwPDB remediated NMR restraints for PDB entry 1pjf" _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 1pjf" save_ save_assembly _Assembly.Sf_category assembly _Assembly.Sf_framecode assembly _Assembly.Entry_ID rr_1pjf _Assembly.ID 1 _Assembly.Name 1pjf _Assembly.Number_of_components 1 _Assembly.Organic_ligands 0 _Assembly.Metal_ions 0 _Assembly.Non_standard_bonds no _Assembly.Paramagnetic no _Assembly.Thiol_state "not present" _Assembly.Molecular_mass 4611.419 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 "COAT PROTEIN B" 1 $COAT_PROTEIN_B A . no . . . . . . rr_1pjf 1 stop_ save_ save_COAT_PROTEIN_B _Entity.Sf_category entity _Entity.Sf_framecode COAT_PROTEIN_B _Entity.Entry_ID rr_1pjf _Entity.ID 1 _Entity.Name COAT_PROTEIN_B _Entity.Type polymer _Entity.Polymer_type polypeptide(L) _Entity.Polymer_strand_ID A _Entity.Polymer_seq_one_letter_code ; GVIDTSAVESAITDGQGDMK AIGGYIVGALVILAVAGLIY SMLRKA ; _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 46 _Entity.Paramagnetic no _Entity.Thiol_state "not present" _Entity.Parent_entity_ID 1 _Entity.Formula_weight 4611.419 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 . GLY . rr_1pjf 1 2 . VAL . rr_1pjf 1 3 . ILE . rr_1pjf 1 4 . ASP . rr_1pjf 1 5 . THR . rr_1pjf 1 6 . SER . rr_1pjf 1 7 . ALA . rr_1pjf 1 8 . VAL . rr_1pjf 1 9 . GLU . rr_1pjf 1 10 . SER . rr_1pjf 1 11 . ALA . rr_1pjf 1 12 . ILE . rr_1pjf 1 13 . THR . rr_1pjf 1 14 . ASP . rr_1pjf 1 15 . GLY . rr_1pjf 1 16 . GLN . rr_1pjf 1 17 . GLY . rr_1pjf 1 18 . ASP . rr_1pjf 1 19 . MET . rr_1pjf 1 20 . LYS . rr_1pjf 1 21 . ALA . rr_1pjf 1 22 . ILE . rr_1pjf 1 23 . GLY . rr_1pjf 1 24 . GLY . rr_1pjf 1 25 . TYR . rr_1pjf 1 26 . ILE . rr_1pjf 1 27 . VAL . rr_1pjf 1 28 . GLY . rr_1pjf 1 29 . ALA . rr_1pjf 1 30 . LEU . rr_1pjf 1 31 . VAL . rr_1pjf 1 32 . ILE . rr_1pjf 1 33 . LEU . rr_1pjf 1 34 . ALA . rr_1pjf 1 35 . VAL . rr_1pjf 1 36 . ALA . rr_1pjf 1 37 . GLY . rr_1pjf 1 38 . LEU . rr_1pjf 1 39 . ILE . rr_1pjf 1 40 . TYR . rr_1pjf 1 41 . SER . rr_1pjf 1 42 . MET . rr_1pjf 1 43 . LEU . rr_1pjf 1 44 . ARG . rr_1pjf 1 45 . LYS . rr_1pjf 1 46 . ALA . rr_1pjf 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 . GLY 1 1 rr_1pjf 1 . VAL 2 2 rr_1pjf 1 . ILE 3 3 rr_1pjf 1 . ASP 4 4 rr_1pjf 1 . THR 5 5 rr_1pjf 1 . SER 6 6 rr_1pjf 1 . ALA 7 7 rr_1pjf 1 . VAL 8 8 rr_1pjf 1 . GLU 9 9 rr_1pjf 1 . SER 10 10 rr_1pjf 1 . ALA 11 11 rr_1pjf 1 . ILE 12 12 rr_1pjf 1 . THR 13 13 rr_1pjf 1 . ASP 14 14 rr_1pjf 1 . GLY 15 15 rr_1pjf 1 . GLN 16 16 rr_1pjf 1 . GLY 17 17 rr_1pjf 1 . ASP 18 18 rr_1pjf 1 . MET 19 19 rr_1pjf 1 . LYS 20 20 rr_1pjf 1 . ALA 21 21 rr_1pjf 1 . ILE 22 22 rr_1pjf 1 . GLY 23 23 rr_1pjf 1 . GLY 24 24 rr_1pjf 1 . TYR 25 25 rr_1pjf 1 . ILE 26 26 rr_1pjf 1 . VAL 27 27 rr_1pjf 1 . GLY 28 28 rr_1pjf 1 . ALA 29 29 rr_1pjf 1 . LEU 30 30 rr_1pjf 1 . VAL 31 31 rr_1pjf 1 . ILE 32 32 rr_1pjf 1 . LEU 33 33 rr_1pjf 1 . ALA 34 34 rr_1pjf 1 . VAL 35 35 rr_1pjf 1 . ALA 36 36 rr_1pjf 1 . GLY 37 37 rr_1pjf 1 . LEU 38 38 rr_1pjf 1 . ILE 39 39 rr_1pjf 1 . TYR 40 40 rr_1pjf 1 . SER 41 41 rr_1pjf 1 . MET 42 42 rr_1pjf 1 . LEU 43 43 rr_1pjf 1 . ARG 44 44 rr_1pjf 1 . LYS 45 45 rr_1pjf 1 . ALA 46 46 rr_1pjf 1 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_1pjf _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 27 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_1pjf _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 1pjf.mr . . "MR format" 1 comment "Not applicable" "Not applicable" 0 rr_1pjf 1 1 1pjf.mr . . n/a 2 comment "Not applicable" "Not applicable" 0 rr_1pjf 1 1 1pjf.mr . . unknown 3 unknown "Not applicable" "Not applicable" 0 rr_1pjf 1 1 1pjf.mr . . "MR format" 4 "nomenclature mapping" "Not applicable" "Not applicable" 0 rr_1pjf 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_1pjf _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 VIRUS/VIRAL PROTEIN 02-JUN-03 1PJF *TITLE SOLID STATE NMR STRUCTURE OF THE PF1 MAJOR COAT PROTEIN IN *TITLE 2 MAGNETICALLY ALIGNED BACTERIOPHAGE *COMPND MOL_ID: 1; *COMPND 2 MOLECULE: COAT PROTEIN B; *COMPND 3 CHAIN: A; *COMPND 4 SYNONYM: MAJOR COAT PROTEIN *SOURCE MOL_ID: 1; *SOURCE 2 ORGANISM_SCIENTIFIC: BACTERIOPHAGE PF1; *SOURCE 3 ORGANISM_COMMON: VIRUS; *SOURCE 4 OTHER_DETAILS: PSEUDOMONAS AERUGINOSA (ATCC #25102) WAS *SOURCE 5 THE HOST BACTERIA. *KEYWDS VIRUS/VIRAL PROTEIN *EXPDTA NMR, 27 STRUCTURES *AUTHOR D.S.THIRIOT, A.A.NEVZOROV, L.ZAGYANSKIY, C.H.WU, S.J.OPELLA *REVDAT 1 10-AUG-04 1PJF 0 ; save_ save_MR_file_comment_2 _Org_constr_file_comment.Sf_framecode MR_file_comment_2 _Org_constr_file_comment.Sf_category org_constr_file_comment _Org_constr_file_comment.Entry_ID rr_1pjf _Org_constr_file_comment.ID 2 _Org_constr_file_comment.Constraint_file_ID 1 _Org_constr_file_comment.Block_ID 2 _Org_constr_file_comment.Details "Generated by Wattos" _Org_constr_file_comment.Comment ; Thiriot, D.S. and Opella, S.J. et al. Summary of constraints used in the calculation of structure 1PJF.pdb For 200 structures calculated: Backbone mean RMSD of family to average structure = 1.056 angstroms For the best 25 structures as assessed by statistical ramachandran potential from pdb structures: Backbone mean RMSD of family to average structure = 0.876 angstroms The monomer structure in 1PJF was selected from the 25 best as the family member with the structure nearest to the average structure. In 1PJF, this is model 1, without sidechains, and is the only backbone conformer represented. All other models are rotations and translations of model 1 to construct a virion model. Structure calculation used the following values. 15N chemical shift tensor: sigma11 64 +/- 7 ppm (all except glycine) sigma22 77 +/- 7 ppm sigma33 222 +/- 7 ppm 15N chemical shift tensor: sigma11 41 +/- 7 ppm (glycine) sigma22 64 +/- 7 ppm sigma33 215 +/- 7 ppm Chemical shift referencing was to external solid powdered 15N ammonium sulfate, defined as 26.8 ppm Bond angles (degrees): gamma 18.5 (angle between the N-H bond and sigma33 axis of 15N chemical shift tensor) HNCa 118.2 NCoCa 115.6 HNCo 119.5 NCaCo 110.5 CaCoO 121.1 NCoO 123.2 Bond lengths (angstroms): CaCo 1.52 CoN 1.33 NCa 1.46 NH 1.07 CoO 1.23 ; save_