6BDU | pdb_00006bdu

Crystal structure of PprA from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb6BDU/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-10-24 Released: 2018-09-05 
• Deposition Author(s): Szabla, R., Czerwinski, M., Junop, M.S.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Crystal structure of PprA from Deinococcus radiodurans

Szabla, R., Czerwinski, M., Junop, M.S.

To be published.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 67.21 kDa 
• Atom Count: 4,446 
• Modeled Residue Count: 538 
• Deposited Residue Count: 614 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein PprA	A, B	307	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 2  Gene Names: pprA, DR_A0346
UniProt
Find proteins for O32504 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore O32504  Go to UniProtKB:  O32504

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.236 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.629	α = 90
b = 99.149	β = 90
c = 116.69	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-09-05 
Deposition Author(s): Szabla, R., Czerwinski, M., Junop, M.S.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	2008R00075

Revision History  

• Version 1.0: 2018-09-05
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Structure summary