2OCD Hydrolase date Dec 20, 2006
title Crystal Structure Of L-Asparaginase I From Vibrio Cholerae O Eltor Str. N16961
authors B.Nocek, R.Wu, J.Osipiuk, S.Moy, Y.Kim, A.Joachimiak, Midwest Cent Structural Genomics (Mcsg)
compound source
Molecule: L-Asparaginase I
Chain: A, B, C, D
Engineered: Yes
 Organism_scientific: Vibrio Cholerae
Organism_taxid: 666
Strain: N16961
Gene: O1 Biovar Eltor
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmcsg7
symmetry Space Group: P 1 21 1
R_factor 0.176 R_Free 0.246
crystal
cell
length a length b length c angle alpha angle beta angle gamma
53.235 117.838 121.431 90.00 91.44 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand ACT, GOL, MSE enzyme
note 2OCD supersedes 2H7K
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (232 Kb) [Save to disk]
  • Biological Unit Coordinates (2ocd.pdb1.gz) 216 Kb
  • LPC: Ligand-Protein Contacts for 2OCD
  • CSU: Contacts of Structural Units for 2OCD
  • Likely Quarternary Molecular Structure file(s) for 2OCD
  • Structure Factors (830 Kb)
  • Retrieve 2OCD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2OCD from S2C, [Save to disk]
  • Re-refined 2ocd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2OCD 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 2OCD
  • 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
  • 3D motif for 2OCD, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ocd_D] [2ocd_A] [2ocd_B] [2ocd] [2ocd_C]
  • SWISS-PROT database: [Q9KQK3]
  • Domain organization of [Q9KQK3_VIBCH] by SWISSPFAM
  • Domain found in 2OCD: [Asparaginase ] by SMART
    • Other resources with information on 2OCD
  • Community annotation for 2OCD 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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