1NIJ Structural Genomics, Unknown Function date Dec 24, 2002
title Yjia Protein
authors P.P.Khil, G.Obmolova, A.Teplyakov, A.J.Howard, G.L.Gilliland, R.D.Camerini-Otero, Structure 2 Function Project (S2f)
compound source
Molecule: Hypothetical Protein Yjia
Chain: A
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Yjia Or B4352
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21 Star (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pdest14
symmetry Space Group: C 1 2 1
R_factor 0.223 R_Free NULL
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.830 66.520 56.150 90.00 114.96 90.00
method X-Ray Diffractionresolution 2.00 Å
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal structure of the Escherichia coli YjiA protein suggests a GTP-dependent regulatory function., Khil PP, Obmolova G, Teplyakov A, Howard AJ, Gilliland GL, Camerini-Otero RD, Proteins 2004 Feb 1;54(2):371-4. PMID:14696199
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (58 Kb) [Save to disk]
  • Biological Unit Coordinates (1nij.pdb1.gz) 53 Kb
  • CSU: Contacts of Structural Units for 1NIJ
  • Likely Quarternary Molecular Structure file(s) for 1NIJ
  • Structure Factors (183 Kb)
  • Retrieve 1NIJ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NIJ from S2C, [Save to disk]
  • Re-refined 1nij structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1NIJ 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 1NIJ
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1NIJ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nija1, region A:2-223 [Jmol] [rasmolscript] [script source]
        - Domain d1nija2, region A:224-318 [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: [1nij_A] [1nij]
  • SWISS-PROT database: [P24203]
  • Domain organization of [YJIA_ECOLI] by SWISSPFAM
  • Domain found in 1NIJ: [CobW_C ] by SMART
  • Other resources with information on 1NIJ
  • Community annotation for 1NIJ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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