5IFY

Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2 -Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose

• PDB DOI: https://doi.org/10.2210/pdb5IFY/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia vietnamiensis G4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-02-26 Released: 2016-03-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.197 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 

Literature

Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2'-Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose

Abendroth, J., Dranow, D.M., Lorimer, D., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 209.54 kDa 
• Atom Count: 14,509 
• Modelled Residue Count: 1,753 
• Deposited Residue Count: 1,830 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A, B, C, D, E, F	305	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_0806 EC: 2.7.7.24
UniProt
Find proteins for A4JC15 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JC15  Go to UniProtKB:  A4JC15

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRH	G [auth A], I [auth B], K [auth C], M [auth D], O [auth E], Q [auth F]	2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE C16 H26 N2 O15 P2 ZOSQFDVXNQFKBY-CGAXJHMRSA-N
UMP	H [auth A], J [auth B], L [auth C], N [auth D], P [auth E], R [auth F]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.197 
• R-Value Work: 0.157 
• R-Value Observed: 0.158 
• Space Group: P 2₁ 2₁ 2
• Diffraction Data: https://doi.org/10.18430/M35IFY

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.6	α = 90
b = 254.72	β = 90
c = 82.05	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description