3VDN

Crystal Structure of VldE, the pseudo-glycosyltransferase, in complex with GDP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal Structure of the VldE, the pseudo-glycosyltransferase, which catalyzes non-glycosidic C-N coupling in Validamycin A biosynthesis

Cavalier, M.C.Yim, Y.-S.Asamizu, S.Neau, D.Mahmud, T.Lee, Y.-H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VldE
B
497Streptomyces hygroscopicus subsp. limoneusGene Names: vldE
Find proteins for Q15JG1 (Streptomyces hygroscopicus subsp. limoneus)
Go to UniProtKB:  Q15JG1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.241 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 84.029α = 90.00
b = 121.037β = 90.00
c = 47.824γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
PHENIXmodel building
PHENIXphasing
XDSdata reduction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-09
    Type: Initial release