3UFM | pdb_00003ufm

Co-crystal structure of Deinococcus radiodurans uracil-DNA glycosylase and the C-terminus of the single-stranded DNA-binding protein

• PDB DOI: https://doi.org/10.2210/pdb3UFM/pdb

• Classification: HYDROLASE
• Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539, Deinococcus radiodurans
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-11-01 Released: 2012-11-07 
• Deposition Author(s): George, N.P., Keck, J.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.208 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.170 (Depositor) 
• R-Value Observed: 
  0.172 (Depositor) 

Literature

Identification of the SSB-interaction platform of Deinococcus radiodurans uracil-DNA glycosylase

George, N.P., Keck, J.L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 30.54 kDa 
• Atom Count: 2,029 
• Modeled Residue Count: 234 
• Deposited Residue Count: 267 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uracil-DNA glycosylase	A	255	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR0689, DR_0689, ung EC: 3.2.2.27
UniProt
Find proteins for Q9RWH9 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RWH9  Go to UniProtKB:  Q9RWH9

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Single-stranded DNA-binding protein	B	12	Deinococcus radiodurans	Mutation(s): 0
UniProt
Find proteins for Q9RY51 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RY51  Go to UniProtKB:  Q9RY51

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	C [auth A], D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.208 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.170 (Depositor) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.343	α = 90
b = 92.64	β = 90
c = 66.012	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-07 
Deposition Author(s): George, N.P., Keck, J.L.

Revision History  

• Version 1.0: 2012-11-07
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.2: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations