3DMP | pdb_00003dmp

2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb3DMP/pdb

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


• Deposited: 2008-07-01 Released: 2008-07-15 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.271 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.221 (Depositor) 

Literature

2.6 A crystal structure of uracil phosphoribosyltransferase from Burkholderia pseudomallei

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.79 kDa 
• Atom Count: 6,777 
• Modeled Residue Count: 855 
• Deposited Residue Count: 868 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil phosphoribosyltransferase	A, B, C, D	217	Burkholderia pseudomallei	Mutation(s): 0  Gene Names: upp, BPSL1166 EC: 2.4.2.9
UniProt
Find proteins for Q63VS8 (Burkholderia pseudomallei (strain K96243)) Explore Q63VS8  Go to UniProtKB:  Q63VS8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.271 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.221 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.222	α = 90
b = 80.637	β = 99.11
c = 141.833	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references