2J2M Oxidoreductase date Aug 17, 2006
title Crystal Structure Analysis Of Catalase From Exiguobacterium Oxidotolerans
authors I.Hara, N.Ichise, K.Kojima, H.Kondo, S.Ohgiya, H.Matsuyama, I.Yumoto
compound source
Molecule: Catalase
Chain: A, B, C, D
Ec: 1.11.1.6
Organism_scientific: Exiguobacterium Oxidotolerans
Organism_taxid: 223958
Strain: T-2-2t
symmetry Space Group: P 1 21 1
R_factor 0.199 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
94.267 131.935 110.642 90.00 107.61 90.00
method X-Ray Diffractionresolution 2.4 Å
ligand HEM enzyme Oxidoreductase E.C.1.11.1.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B
  • catalase activity
  • peroxidase activity


  • Primary referenceRelationship between the size of the bottleneck 15 A from iron in the main channel and the reactivity of catalase corresponding to the molecular size of substrates., Hara I, Ichise N, Kojima K, Kondo H, Ohgiya S, Matsuyama H, Yumoto I, Biochemistry. 2007 Jan 9;46(1):11-22. PMID:17198371
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (330 Kb) [Save to disk]
  • Biological Unit Coordinates (2j2m.pdb1.gz) 323 Kb
  • LPC: Ligand-Protein Contacts for 2J2M
  • CSU: Contacts of Structural Units for 2J2M
  • Likely Quarternary Molecular Structure file(s) for 2J2M
  • Structure Factors (775 Kb)
  • Retrieve 2J2M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2J2M from S2C, [Save to disk]
  • Re-refined 2j2m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2J2M 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 2J2M
  • 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 2J2M, from MSDmotif at EBI
  • Fold representative 2j2m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2j2m_D] [2j2m_C] [2j2m_A] [2j2m_B] [2j2m]
  • SWISS-PROT database: [A2A136]
  • Domain organization of [A2A136_9BACL] by SWISSPFAM
  • Domain found in 2J2M: [Catalase ] by SMART
  • Other resources with information on 2J2M
  • Community annotation for 2J2M 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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