8U1J

N-Terminal domain of DNA-Damage Response Protein C (DdrC) from Deinococcus radiodurans - Crystal form xMJ7102

PDB DOI: https://doi.org/10.2210/pdb8U1J/pdb

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

Deposited: 2023-09-01 Released: 2023-09-20
Deposition Author(s): Szabla, R., Song, Y., Junop, M.S.
Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.257
R-Value Work: 0.225
R-Value Observed: 0.227

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Full-length dimer of DNA-Damage Response Protein C from Deinococcus radiodurans

Szabla, R., Li, M.C., Junop, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 14.4 kDa
Atom Count: 748
Modelled Residue Count: 98
Deposited Residue Count: 129
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 damage response protein C	A	129	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0 Gene Names: ddrC
UniProt
Find proteins for Q9RYE6 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RYE6 Go to UniProtKB: Q9RYE6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9RYE6
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.257
R-Value Work: 0.225
R-Value Observed: 0.227
Space Group: I 4₁ 2 2
Diffraction Data: https://doi.org/10.5281/zenodo.8309780

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.41	α = 90
b = 73.41	β = 90
c = 110.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxDC	data collection
autoPROC	data processing
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
BUCCANEER	model building

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-09-20

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: 2023-09-20
Type: Initial release
Version 1.1: 2023-11-15
Changes: Data collection

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.