3UBR Oxidoreductase date Oct 24, 2011
title Laue Structure Of Shewanella Oneidensis Cytochrome-C Nitrite
authors M.Youngblut, E.T.Judd, V.Srajer, B.Sayed, T.Goeltzner, S.Elliott, M.Schmidt, A.Pacheco
compound source
Molecule: Cytochrome C-552
Chain: A, B
Synonym: Ammonia-Forming Cytochrome C Nitrite Reductase, Cy Nitrite Reductase;
Ec: 1.7.2.2
Engineered: Yes
Organism_scientific: Shewanella Oneidensis
Organism_taxid: 70863
Gene: Nrfa, Shewanella Oneidensis, So_3980
Expression_system: Shewanella
Expression_system_taxid: 22
symmetry Space Group: P 21 21 21
R_factor 0.190 R_Free 0.285
crystal
cell
length a length b length c angle alpha angle beta angle gamma
51.500 95.900 223.800 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.59 Å
ligand CA, HEC enzyme Oxidoreductase E.C.1.7.2.2 BRENDA
Gene SO
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceLaue crystal structure of Shewanella oneidensis cytochrome c nitrite reductase from a high-yield expression system., Youngblut M, Judd ET, Srajer V, Sayyed B, Goelzer T, Elliott SJ, Schmidt M, Pacheco AA, J Biol Inorg Chem. 2012 Mar 2. PMID:22382353
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (158 Kb) [Save to disk]
  • Biological Unit Coordinates (3ubr.pdb1.gz) 148 Kb
  • LPC: Ligand-Protein Contacts for 3UBR
  • CSU: Contacts of Structural Units for 3UBR
  • Structure Factors (395 Kb)
  • Retrieve 3UBR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3UBR from S2C, [Save to disk]
  • Re-refined 3ubr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3UBR 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 3UBR
  • 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 3UBR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3ubr] [3ubr_B] [3ubr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 3UBR
  • Community annotation for 3UBR at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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