1Y67 Oxidoreductase date Dec 03, 2004
title Crystal Structure Of Manganese Superoxide Dismutase From Dei Radiodurans
authors S.Chan, S.Tanaka, M.R.Sawaya, L.J.Perry
compound source
Molecule: Manganese Superoxide Dismutase
Chain: A, B, C, D
Synonym: Mnsod
Ec: 1.15.1.1
Engineered: Yes
Organism_scientific: Deinococcus Radiodurans
Organism_taxid: 1299
Gene: Soda
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21-Gold (De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: P 1 21 1
R_factor 0.184 R_Free 0.205
crystal
cell
length a length b length c angle alpha angle beta angle gamma
43.801 87.922 116.198 90.00 91.14 90.00
method X-Ray Diffractionresolution 1.85 Å
ligand FE enzyme Oxidoreductase E.C.1.15.1.1 BRENDA
related structures by homologous chain: 1D5N, 1EN4
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • superoxide dismutase activit...


  • Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (1y67.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (1y67.pdb2.gz) 71 Kb
  • LPC: Ligand-Protein Contacts for 1Y67
  • CSU: Contacts of Structural Units for 1Y67
  • Likely Quarternary Molecular Structure file(s) for 1Y67
  • Structure Factors (612 Kb)
  • Retrieve 1Y67 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1Y67 from S2C, [Save to disk]
  • Re-refined 1y67 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1Y67 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 1Y67
  • 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 1Y67, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1y67a1, region A:2-89 [Jmol] [rasmolscript] [script source]
        - Domain d1y67a2, region A:98-213 [Jmol] [rasmolscript] [script source]
        - Domain d1y67b1, region B:2-89 [Jmol] [rasmolscript] [script source]
        - Domain d1y67b2, region B:98-211 [Jmol] [rasmolscript] [script source]
        - Domain d1y67c1, region C:2-89 [Jmol] [rasmolscript] [script source]
        - Domain d1y67c2, region C:98-213 [Jmol] [rasmolscript] [script source]
        - Domain d1y67d1, region D:2-89 [Jmol] [rasmolscript] [script source]
        - Domain d1y67d2, region D:98-213 [Jmol] [rasmolscript] [script source]
  • Fold representative 1y67 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1y67_C] [1y67_D] [1y67_B] [1y67_A] [1y67]
  • SWISS-PROT database: [Q9RUV2]
  • Domain organization of [SODM_DEIRA] by SWISSPFAM
  • Other resources with information on 1Y67
  • Community annotation for 1Y67 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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