4E4E Oxidoreductase date Mar 12, 2012
title Crystal Structure Of The Y34f Mutant Of Saccharomyces Cerevi Manganese Superoxide Dismutase
authors Y.Sheng, D.Cascio, J.S.Valentine
compound source
Molecule: Superoxide Dismutase [Mn], Mitochondrial
Chain: A, B, C, D
Ec: 1.15.1.1
Engineered: Yes
Mutation: Yes
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Eg110
Gene: Sod2, Yhr008c
Expression_system: Saccharomyces Cerevisiae
Expression_system_taxid: 4932
Expression_system_strain: Eg110
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Yep352
symmetry Space Group: P 1
R_factor 0.190 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
61.139 63.022 63.943 112.19 106.78 103.88
method X-Ray Diffractionresolution 1.88 Å
ligand MLY, MN enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceSix-coordinate manganese(3+) in catalysis by yeast manganese superoxide dismutase., Sheng Y, Butler Gralla E, Schumacher M, Cascio D, Cabelli DE, Selverstone Valentine J, Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14314-9. Epub 2012 Aug 20. PMID:22908245
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (150 Kb) [Save to disk]
  • Biological Unit Coordinates (4e4e.pdb1.gz) 139 Kb
  • LPC: Ligand-Protein Contacts for 4E4E
  • CSU: Contacts of Structural Units for 4E4E
  • Structure Factors (832 Kb)
  • Retrieve 4E4E in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4E4E from S2C, [Save to disk]
  • Re-refined 4e4e structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4E4E 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 4E4E
  • 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 4E4E, from MSDmotif at EBI
  • Fold representative 4e4e from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4e4e_D] [4e4e_C] [4e4e] [4e4e_A] [4e4e_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 4E4E
  • Community annotation for 4E4E at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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