3BFR Oxidoreductase date Nov 23, 2007
title The Crystal Structure Of Sod2 From Saccharomyces Cerevisiae
authors Y.X.He, M.X.Zhao, C.Zhou
compound source
Molecule: Superoxide Dismutase [Mn]
Chain: A
Ec: 1.15.1.1
Engineered: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_taxid: 4932
Strain: S288c
Gene: Sod2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a
symmetry Space Group: P 2 3
R_factor 0.195 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.740 92.740 92.740 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.05 Å
ligand MN3 enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructures of native and Fe-substituted SOD2 from Saccharomyces cerevisiae., Kang Y, He YX, Zhao MX, Li WF, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011 Oct 1;67(Pt 10):1173-8., Epub 2011 Sep 24. PMID:22102021
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (40 Kb) [Save to disk]
  • Biological Unit Coordinates (3bfr.pdb1.gz) 136 Kb
  • LPC: Ligand-Protein Contacts for 3BFR
  • CSU: Contacts of Structural Units for 3BFR
  • Likely Quarternary Molecular Structure file(s) for 3BFR
  • Structure Factors (910 Kb)
  • Retrieve 3BFR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BFR from S2C, [Save to disk]
  • Re-refined 3bfr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BFR 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 3BFR
  • 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 3BFR, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bfr_A] [3bfr]
  • SWISS-PROT database: [P00447]
  • Domain organization of [SODM_YEAST] by SWISSPFAM
  • Other resources with information on 3BFR
  • Community annotation for 3BFR 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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