3VDM | pdb_00003vdm

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

• PDB DOI: https://doi.org/10.2210/pdb3VDM/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces hygroscopicus subsp. limoneus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-05 Released: 2013-01-09 
• Deposition Author(s): Cavalier, M.C., Yim, Y.-S., Asamizu, S., Neau, D., Mahmud, T., Lee, Y.-H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Crystal Structure of 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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.01 kDa 
• Atom Count: 7,963 
• Modeled Residue Count: 957 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VldE	A, B	497	Streptomyces hygroscopicus subsp. limoneus	Mutation(s): 0  Gene Names: vldE EC: 2.4 (PDB Primary Data), 2.5.1.135 (UniProt)
UniProt
Find proteins for Q15JG1 (Streptomyces hygroscopicus subsp. limoneus) Explore Q15JG1  Go to UniProtKB:  Q15JG1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.222 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.237	α = 90
b = 48.562	β = 91.88
c = 123.049	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-09 
Deposition Author(s): Cavalier, M.C., Yim, Y.-S., Asamizu, S., Neau, D., Mahmud, T., Lee, Y.-H.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Data collection, Database references