4LHR | pdb_00004lhr

Crystal structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase from Burkholderia thailandensis

• PDB DOI: https://doi.org/10.2210/pdb4LHR/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia thailandensis E264
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-07-01 Released: 2013-08-07 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.135 (Depositor), 0.150 (DCC) 
• R-Value Work: 
  0.117 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.118 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a deoxyuridine 5'-triphosphate nucleotidohydrolase from Burkholderia thailandensis

Edwards, T.E., Abendroth, J., Seattle Structural Genomics Center for Infectious Disease

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 17.03 kDa 
• Atom Count: 1,256 
• Modeled Residue Count: 134 
• Deposited Residue Count: 156 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	156	Burkholderia thailandensis E264	Mutation(s): 0  Gene Names: BTH_I0767, dut EC: 3.6.1.23
UniProt
Find proteins for Q2T0H6 (Burkholderia thailandensis (strain ATCC 700388 / DSM 13276 / CCUG 48851 / CIP 106301 / E264)) Explore Q2T0H6  Go to UniProtKB:  Q2T0H6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	B [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.135 (Depositor), 0.150 (DCC) 
• R-Value Work:  0.117 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.118 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34LHR

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.36	α = 90
b = 84.36	β = 90
c = 54.62	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2017-10-11
  Changes: Data collection
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description