2NYB Oxidoreductase date Nov 20, 2006
title Crystal Structure Of E.Coli Iron Superoxide Dismutase Q69e A Angstrom Resolution
authors J.C.Porta, A.Vahedi-Faridi, G.E.O.Borgstahl
compound source
Molecule: Superoxide Dismutase [Fe]
Chain: A, B, C, D
Synonym: Iron Superoxide Dismutase
Engineered: Yes
Mutation: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 562
Gene: Sodb, B1656, Jw1648
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.160 R_Free 0.174
length a length b length c angle alpha angle beta angle gamma
43.508 107.596 84.120 90.00 94.89 90.00
method X-Ray Diffractionresolution 1.10 Å
ligand FE2, O enzyme Oxidoreductase E.C. BRENDA
A, D, C, B

Primary referenceHow can a single second sphere amino acid substitution cause reduction midpoint potential changes of hundreds of millivolts?, Yikilmaz E, Porta J, Grove LE, Vahedi-Faridi A, Bronshteyn Y, Brunold TC, Borgstahl GE, Miller AF, J Am Chem Soc. 2007 Aug 15;129(32):9927-40. Epub 2007 Jul 12. PMID:17628062
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (306 Kb) [Save to disk]
  • Biological Unit Coordinates (2nyb.pdb1.gz) 154 Kb
  • Biological Unit Coordinates (2nyb.pdb2.gz) 150 Kb
  • LPC: Ligand-Protein Contacts for 2NYB
  • CSU: Contacts of Structural Units for 2NYB
  • Likely Quarternary Molecular Structure file(s) for 2NYB
  • Structure Factors (2019 Kb)
  • Retrieve 2NYB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2NYB from S2C, [Save to disk]
  • Re-refined 2nyb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2NYB 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 2NYB
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2NYB, from MSDmotif at EBI
  • Fold representative 2nyb from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2nyb_A] [2nyb] [2nyb_C] [2nyb_D] [2nyb_B]
  • SWISS-PROT database: [P0AGD3]
  • Domain organization of [SODF_ECOLI] by SWISSPFAM
  • Other resources with information on 2NYB
  • Community annotation for 2NYB at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science