1ZNO

Crystal Structure of VC702 from Vibrio Cholerae, Northeast Structural Genomics Consortium Target: VcP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.230 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of VC0702 at 2.0 A: conserved hypothetical protein from Vibrio cholerae.

Ni, S.Forouhar, F.Bussiere, D.E.Robinson, H.Kennedy, M.A.

(2006) Proteins 63: 733-741

  • DOI: 10.1002/prot.20919

  • PubMed Abstract: 
  • VC0702, a conserved hypothetical protein of unknown function from Vibrio cholerae, resides in a three-gene operon containing the MbaA gene that encodes for a GGDEF and EAL domain-containing protein which is involved in regulating formation of the ext ...

    VC0702, a conserved hypothetical protein of unknown function from Vibrio cholerae, resides in a three-gene operon containing the MbaA gene that encodes for a GGDEF and EAL domain-containing protein which is involved in regulating formation of the extracellular matrix of biofilms in Vibrio cholerae. The VC0702 crystal structure has been determined at 2.0 A and refined to Rwork = 22.8% and Rfree = 26.3%. VC0702 crystallized in an orthorhombic crystal lattice in the C222(1) space group with dimensions of a = 66.61 A, b = 88.118 A, and c = 118.35 A with a homodimer in the asymmetric unit. VC0702, which forms a mixed alpha + beta three-layered alphabetaalpha sandwich, belongs to the Pfam DUF84 and COG1986 families of proteins. Sequence conservation within the DUF84 and COG1986 families was used to identify a conserved patch of surface residues that define a cleft and potential substrate-binding site in VC0702. The three-dimensional structure of VC0702 is similar to that of Mj0226 from Methanococcus janeschii, which has been identified as a novel NTPase that binds NTP in a deep cleft similarly located to the conserved patch of surface residues that define an analogous cleft in VC0702. Collectively, the data suggest that VC0702 may have a biochemical function that involves NTP binding and phosphatase activity of some kind, and is likely involved in regulation of the signaling pathway that controls biofilm formation and maintenance in Vibrio cholerae.


    Organizational Affiliation

    Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Hypothetical UPF0244 protein VC0702
A, B
183Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)EC: 3.6.1.-
Find proteins for Q9KU27 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Go to UniProtKB:  Q9KU27
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 66.611α = 90.00
b = 88.118β = 90.00
c = 118.355γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance