2VPA Oxidoreductase date Feb 27, 2008
title High Resolution Crystal Structure Of The Antibiotic Resistan Nima From Deinococcus Radiodurans
authors H.K.S.Leiros, C.Tedesco, S.M.Mcsweeney
compound source
Molecule: Nima-Related Protein
Chain: A
Synonym: 5-Nitroimidazole Reductase
Engineered: Yes
Other_details: Includes The First 10 Residues Of The 21 Res N-Terminal His Tag
 Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plyss
symmetry Space Group: C 1 2 1
R_factor 0.141 R_Free 0.180
crystal
cell
length a length b length c angle alpha angle beta angle gamma
100.037 38.951 59.897 90.00 114.36 90.00
method X-Ray Diffractionresolution 1.20 Å
ligand ACT, PYR enzyme
note 2VPA is a representative structure
Primary referenceHigh-resolution structure of the antibiotic resistance protein NimA from Deinococcus radiodurans., Leiros HK, Tedesco C, McSweeney SM, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jun 1;64(Pt 6):442-7. doi:, 10.1107/S1744309108009901. Epub 2008 May 16. PMID:18540048
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (2vpa.pdb1.gz) 167 Kb
  • LPC: Ligand-Protein Contacts for 2VPA
  • CSU: Contacts of Structural Units for 2VPA
  • Likely Quarternary Molecular Structure file(s) for 2VPA
  • Structure Factors (1080 Kb)
  • Retrieve 2VPA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VPA from S2C, [Save to disk]
  • Re-refined 2vpa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2VPA 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 2VPA
  • 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 2VPA, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vpa_A] [2vpa]
  • SWISS-PROT database: [Q9RW27]
  • Domain organization of [Q9RW27_DEIRA] by SWISSPFAM
    • Other resources with information on 2VPA
  • Community annotation for 2VPA 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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