3DC6 Oxidoreductase date Jun 03, 2008
title Crystal Structure Of A Manganese Superoxide Dismutases From Caenorhabditis Elegans
authors C.H.Trinh, T.Hunter, E.E.Stewart, S.E.V.Phillips, G.J.Hunter
compound source
Molecule: Superoxide Dismutase [Mn] 1
Chain: A, C
Ec: 1.15.1.1
Engineered: Yes
Organism_scientific: Caenorhabditis Elegans
Organism_common: Nematode
Organism_taxid: 6239
Gene: Sod-2, Sdm-1, F10d11.1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ox326a
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Ptrc-99a
symmetry Space Group: P 41 21 2
R_factor 0.169 R_Free 0.201
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.980 80.980 137.444 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand MN, SO4 enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, C


Primary referencePurification, crystallization and X-ray structures of the two manganese superoxide dismutases from Caenorhabditis elegans., Trinh CH, Hunter T, Stewart EE, Phillips SE, Hunter GJ, Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Dec 1;64(Pt, 12):1110-4. Epub 2008 Nov 28. PMID:19052361
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (3dc6.pdb1.gz) 143 Kb
  • LPC: Ligand-Protein Contacts for 3DC6
  • CSU: Contacts of Structural Units for 3DC6
  • Likely Quarternary Molecular Structure file(s) for 3DC6
  • Structure Factors (320 Kb)
  • Retrieve 3DC6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DC6 from S2C, [Save to disk]
  • Re-refined 3dc6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DC6 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 3DC6
  • 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 3DC6, from MSDmotif at EBI
  • Fold representative 3dc6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dc6_A] [3dc6] [3dc6_C]
  • SWISS-PROT database: [P31161]
  • Domain organization of [SODM1_CAEEL] by SWISSPFAM
  • Other resources with information on 3DC6
  • Community annotation for 3DC6 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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