3MDX | pdb_00003mdx

Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, rhombohedral crystal form

• PDB DOI: https://doi.org/10.2210/pdb3MDX/pdb

• Classification: HYDROLASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-03-31 Released: 2010-04-21 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.151 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of deoxyuridine 5-triphosphate nucleotidohydrolase from Brucella melitensis, rhombohedral crystal form

Abendroth, J., Gardberg, A.S., Staker, B.

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: 19.03 kDa 
• Atom Count: 1,257 
• Modeled Residue Count: 139 
• Deposited Residue Count: 178 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A	178	Brucella abortus 2308	Mutation(s): 0  Gene Names: dut, BAB1_1687 EC: 3.6.1.23
UniProt
Find proteins for Q2YRG4 (Brucella abortus (strain 2308)) Explore Q2YRG4  Go to UniProtKB:  Q2YRG4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	B [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.167 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.150 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.151 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33MDX

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.88	α = 90
b = 67.88	β = 90
c = 95.89	γ = 120

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description