5IDT | pdb_00005idt

Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Burkholderia vietnamiensis with bound Thymidine

• PDB DOI: https://doi.org/10.2210/pdb5IDT/pdb

• Classification: TRANSFERASE
• Organism(s): Burkholderia vietnamiensis G4
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-02-24 Released: 2016-03-09 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.178 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of a Glucose-1-phosphate Thymidylyltransferase from Burkholderia vietnamiensis with bound Thymidine

Dranow, D.M., Hornayi, P.S., Lorimer, D.D., Edwards, T.E.

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)

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 134.07 kDa 
• Atom Count: 8,678 
• Modeled Residue Count: 1,153 
• Deposited Residue Count: 1,208 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucose-1-phosphate thymidylyltransferase	A, B, C, D	302	Burkholderia vietnamiensis G4	Mutation(s): 0  Gene Names: Bcep1808_3215 EC: 2.7.7.24
UniProt
Find proteins for A4JIV2 (Burkholderia vietnamiensis (strain G4 / LMG 22486)) Explore A4JIV2  Go to UniProtKB:  A4JIV2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
THM	E [auth A], J [auth D]	THYMIDINE C10 H14 N2 O5 IQFYYKKMVGJFEH-XLPZGREQSA-N
EDO	F [auth A], G [auth A], H [auth A], I [auth B], K [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.231 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.176 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.178 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M35IDT

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.11	α = 90
b = 114.86	β = 90.58
c = 95.78	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MoRDa	phasing

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