9OM8 | pdb_00009om8

Crystal structure of PprA S-F filament from Deinococcus radiodurans

• PDB DOI: https://doi.org/10.2210/pdb9OM8/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2025-05-13 Released: 2025-05-28 
• Deposition Author(s): Szabla, R., Junop, M.S., Wood, K.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free: 
  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.213 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: in silico

Literature

Self-assembly of PprA from D.radiodurans

Szabla, R., Junop, M.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 16-mer - A16 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 119.15 kDa 
• Atom Count: 7,449 
• Modeled Residue Count: 1,003 
• Deposited Residue Count: 1,108 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein PprA	A, B, C, D	277	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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.83 Å
• R-Value Free:  0.275 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.213 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Diffraction Data: https://doi.org/10.5281/zenodo.15399126

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 298.84	α = 90
b = 44.487	β = 106.626
c = 89.751	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
PHENIX	phasing
PHENIX	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Szabla, R., Junop, M.S., Wood, K.

---

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

Revision History  

• Version 1.0: 2025-05-28
  Type: Initial release