3WAG | pdb_00003wag

Crystal structure of glycosyltransferase VinC in complex with DTDP

• PDB DOI: https://doi.org/10.2210/pdb3WAG/pdb

• Classification: TRANSFERASE
• Organism(s): Streptomyces halstedii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-05-02 Released: 2014-06-04 
• Deposition Author(s): Nango, E., Minami, A., Kumasaka, T., Eguchi, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Glycosyltransferase VinC Involved in the Biosynthesis of Vicenistatin

Nango, E., Minami, A., Kumasaka, T., Eguchi, T.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 93.34 kDa 
• Atom Count: 6,629 
• Modeled Residue Count: 800 
• Deposited Residue Count: 838 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosyltransferase	A, B	419	Streptomyces halstedii	Mutation(s): 0  Gene Names: vinC
UniProt
Find proteins for Q76KZ6 (Streptomyces halstedii) Explore Q76KZ6  Go to UniProtKB:  Q76KZ6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TYD	C [auth A], F [auth B]	THYMIDINE-5'-DIPHOSPHATE C10 H16 N2 O11 P2 UJLXYODCHAELLY-XLPZGREQSA-N
PO4	D [auth A], G [auth B], H [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.256 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.829	α = 90
b = 130.162	β = 90
c = 139.787	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Nango, E., Minami, A., Kumasaka, T., Eguchi, T.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description