9YUP | pdb_00009yup

Crystal structure of PprA S-F-S tetramer from Deinococcus radiodurans

PDB DOI: https://doi.org/10.2210/pdb9YUP/pdb

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

Deposited: 2025-10-22 Released: 2025-10-29
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: 2.07 Å
R-Value Free:
0.236 (Depositor), 0.237 (DCC)
R-Value Work:
0.211 (Depositor), 0.212 (DCC)
R-Value Observed:
0.212 (Depositor)

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: 134.98 kDa
Atom Count: 8,655
Modeled Residue Count: 1,113
Deposited Residue Count: 1,228
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, C, D	307	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

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FLC Query on FLC Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth C] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C]	E [auth A], F [auth C], G [auth C]	CITRATE ANION C₆ H₅ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-K		Interactions Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth C] Interactions & Density Focus chain E [auth A] Focus chain F [auth C] Focus chain G [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.07 Å
R-Value Free: 0.236 (Depositor), 0.237 (DCC)
R-Value Work: 0.211 (Depositor), 0.212 (DCC)
R-Value Observed: 0.212 (Depositor)

Diffraction Data: https://doi.org/10.5281/zenodo.17420657

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.679	α = 90
b = 123.221	β = 93.687
c = 139.288	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-10-29

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: 2025-10-29
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.