3VCR Structural Genomics, Unknown Function date Jan 04, 2012
title Crystal Structure Of A Putative Kdpg (2-Keto-3-Deoxy-6- Phosphogluconate) Aldolase From Oleispira Antarctica
authors P.J.Stogios, O.Kagan, R.Di Leo, V.Yim, A.Joachimiak, A.M.Edwards, A.Savchenko, Midwest Center For Structural Genomics (Mcsg)
compound source
Molecule: Putative Kdpg (2-Keto-3-Deoxy-6-Phosphogluconate)
Chain: A, B
Engineered: Yes
 Organism_scientific: Oleispira Antarctica
Organism_taxid: 188908
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: P15tv-L
symmetry Space Group: H 3
R_factor 0.178 R_Free 0.214
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.020 76.020 241.121 90.00 90.00 120.00
method X-Ray Diffractionresolution 1.84 Å
ligand MSE, PYR enzyme
note 3VCR supersedes 3LAB
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceGenome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica., Kube M, Chernikova TN, Al-Ramahi Y, Beloqui A, Lopez-Cortez N, Guazzaroni ME, Heipieper HJ, Klages S, Kotsyurbenko OR, Langer I, Nechitaylo TY, Lunsdorf H, Fernandez M, Juarez S, Ciordia S, Singer A, Kagan O, Egorova O, Alain Petit P, Stogios P, Kim Y, Tchigvintsev A, Flick R, Denaro R, Genovese M, Albar JP, Reva ON, Martinez-Gomariz M, Tran H, Ferrer M, Savchenko A, Yakunin AF, Yakimov MM, Golyshina OV, Reinhardt R, Golyshin PN, Nat Commun. 2013 Jul 23;4:2156. doi: 10.1038/ncomms3156. PMID:23877221
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk]
  • Biological Unit Coordinates (3vcr.pdb1.gz) 156 Kb
  • Biological Unit Coordinates (3vcr.pdb2.gz) 155 Kb
  • LPC: Ligand-Protein Contacts for 3VCR
  • CSU: Contacts of Structural Units for 3VCR
  • Structure Factors (691 Kb)
  • Retrieve 3VCR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3VCR from S2C, [Save to disk]
  • Re-refined 3vcr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3VCR 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 3VCR
  • 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 3VCR, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3vcr_B] [3vcr] [3vcr_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3VCR
  • Community annotation for 3VCR at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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