9YI3 | pdb_00009yi3

Crystal structure of PprA S-F filament from Deinococcus radiodurans

PDB DOI: https://doi.org/10.2210/pdb9YI3/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Deinococcus radiodurans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2025-10-01 Released: 2025-10-15
Deposition Author(s): Szabla, R., Junop, M.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free:
0.275 (Depositor), 0.274 (DCC)
R-Value Work:
0.262 (Depositor), 0.262 (DCC)
R-Value Observed:
0.262 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Self-assembly of PprA from D.radiodurans

Szabla, R., Junop, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 59.84 kDa
Atom Count: 4,318
Modeled Residue Count: 552
Deposited Residue Count: 552
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair protein PprA	A, B	276	Deinococcus radiodurans	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O32504
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.82 Å
R-Value Free: 0.275 (Depositor), 0.274 (DCC)
R-Value Work: 0.262 (Depositor), 0.262 (DCC)
R-Value Observed: 0.262 (Depositor)

Diffraction Data: https://doi.org/10.5281/zenodo.17245629

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.425	α = 90
b = 147.348	β = 90
c = 44.473	γ = 90

Software Package:

Software Name	Purpose
JDirector	data collection
autoPROC	data processing
XDS	data reduction
Aimless	data scaling
pointless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-15

Deposition Author(s):

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

Revision History (Full details and data files)

Version 1.0: 2025-10-15
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.