4DYW | pdb_00004dyw

Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei

• PDB DOI: https://doi.org/10.2210/pdb4DYW/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia pseudomallei 1710b
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-02-29 Released: 2012-04-11 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.251 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of MutT NUDIX hydrolase from Burkholderia pseudomallei

Edwards, T.E., Clifton, M.C., Seattle Structural Genomics Center for Infectious Disease (SSGCID)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 34.67 kDa 
• Atom Count: 2,003 
• Modeled Residue Count: 258 
• Deposited Residue Count: 314 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MutT/NUDIX family protein	A, B	157	Burkholderia pseudomallei 1710b	Mutation(s): 0  Gene Names: BURPS1710b_0547
UniProt
Find proteins for Q3JWU2 (Burkholderia pseudomallei (strain 1710b)) Explore Q3JWU2  Go to UniProtKB:  Q3JWU2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.251 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M34DYW

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.04	α = 90
b = 78.04	β = 90
c = 113.92	γ = 90

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: 2012-04-11 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Refinement description