1J9I Viral Protein date May 25, 2001
title Structure Of The Dna Binding Domain Of The Gpnu1 Subunit Of Terminase
authors T.De Beer, J.Meyer, M.Ortega, Q.Yang, L.Maes, C.Duffy, N.Berton, J. M.Overduin, M.Feiss, C.Catalano
compound source
Molecule: Terminase Small Subunit
Chain: A, B
Fragment: Dna Binding Domain, Residues 1-68
Synonym: Dna Packaging Protein Nu1; Gpnu1 Dbd
Engineered: Yes
 Organism_scientific: Enterobacteria Phage Lambda
Organism_taxid: 10710
Gene: Nu1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
methodSolution NMR
note 1J9I is a representative structure
Primary referenceInsights into specific DNA recognition during the assembly of a viral genome packaging machine., de Beer T, Fang J, Ortega M, Yang Q, Maes L, Duffy C, Berton N, Sippy J, Overduin M, Feiss M, Catalano CE, Mol Cell 2002 May;9(5):981-91. PMID:12049735
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (733 Kb) [Save to disk]
  • Biological Unit Coordinates (1j9i.pdb1.gz) 36 Kb
  • CSU: Contacts of Structural Units for 1J9I
  • Original NMR restraints for 1J9I from PDB
  • Experimental data, such as chemical shifts, at BioMagResBank (BMRB)
  • NMR Restraints Grid from BioMagResBank (BMRB)
  • Retrieve 1J9I in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1J9I from S2C, [Save to disk]
    • View 1J9I in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1J9I
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1J9I, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1j9ia_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1j9ib_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1j9i_A] [1j9i] [1j9i_B]
  • SWISS-PROT database: [P03707]
  • Domain organization of [TERS_LAMBD] by SWISSPFAM
    • Other resources with information on 1J9I
  • Community annotation for 1J9I at PDBWiki (http://pdbwiki.org)
  • NMR Ensemble (OLDERADO: core, domain and representative structure database)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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