2W4E

Structure of an N-terminally truncated Nudix hydrolase DR2204 from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb2W4E/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2008-11-25 Released: 2009-12-01 
• Deposition Author(s): Goncalves, A.M.D., Fioravanti, E., Stelter, M., McSweeney, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Structure of an N-Terminally Truncated Nudix Hydrolase Dr2204 from Deinococcus Radiodurans.

Goncalves, A.M.D., Fioravanti, E., Stelter, M., Mcsweeney, S.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1083

• PubMed: 19923723 
• DOI: https://doi.org/10.1107/S1744309109037191
• Primary Citation of Related Structures:  
  2W4E


• PubMed Abstract: 
  

  Nudix pyrophosphatases are a well represented protein family in the Deinococcus radiodurans genome. These hydrolases, which are known to be enzymatically active towards nucleoside diphosphate derivatives, play a role in cleansing the cell pool of potentially deleterious damage products. Here, the structure of DR2204, the only ADP-ribose pyrophosphatase in the D. radiodurans genome that is known to be active towards flavin adenosine dinucleotide (FAD), is presented at 2.0 angstrom resolution.

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Organizational Affiliation: 

Macromolecular Crystallography Group, European Synchrotron Radiation Facility, Grenoble, France.

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)

Macromolecule Content

• Total Structure Weight: 31.21 kDa 
• Atom Count: 2,178 
• Modelled Residue Count: 268 
• Deposited Residue Count: 290 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MUTT/NUDIX FAMILY PROTEIN	A, B	145	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  EC: 3.6.1.13
UniProt
Find proteins for Q9RSC1 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RSC1  Go to UniProtKB:  Q9RSC1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.247 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.301	α = 90
b = 61.301	β = 90
c = 165.752	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
SHARP	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-01 
Deposition Author(s): Goncalves, A.M.D., Fioravanti, E., Stelter, M., McSweeney, S.

Revision History  

• Version 1.0: 2009-12-01
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance