3ODH Hydrolase Dna date Aug 11, 2010
title Structure Of Okraidna Complex
authors E.S.Vanamee, A.K.Aggarwal
compound source
Molecule: Okrai Endonuclease
Chain: A, B, E, F
Engineered: Yes
 Organism_scientific: Oceanobacter Kriegii
Organism_taxid: 64972
Strain: Neb Strain Collection
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Er2566

Molecule: Dna (5'-D(Tpaptpgpgpaptpcpcpaptpa)-3'
Chain: C, D, G, H
Engineered: Yes
Synthetic: Yes
symmetry Space Group: P 21 21 21
R_factor 0.155 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
80.982 83.075 119.670 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand CA enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B


Primary referenceAsymmetric DNA recognition by the OkrAI endonuclease, an isoschizomer of BamHI., Vanamee ES, Viadiu H, Chan SH, Ummat A, Hartline AM, Xu SY, Aggarwal AK, Nucleic Acids Res. 2010 Sep 9. PMID:20833632
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (292 Kb) [Save to disk]
  • Biological Unit Coordinates (3odh.pdb1.gz) 142 Kb
  • Biological Unit Coordinates (3odh.pdb2.gz) 144 Kb
  • LPC: Ligand-Protein Contacts for 3ODH
  • CSU: Contacts of Structural Units for 3ODH
  • Structure Factors (462 Kb)
  • Retrieve 3ODH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3ODH from S2C, [Save to disk]
  • Re-refined 3odh structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3ODH 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 3ODH
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3ODH, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3odh_D] [3odh_G] [3odh_E] [3odh_A] [3odh] [3odh_C] [3odh_F] [3odh_B] [3odh_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3ODH
  • Community annotation for 3ODH 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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