4TRT

Deinococcus radiodurans DNA polymerase III subunit beta

• PDB DOI: https://doi.org/10.2210/pdb4TRT/pdb

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


• Deposited: 2014-06-17 Released: 2015-04-29 
• Deposition Author(s): Niiranen, L., Lian, K., Johnson, K.A., Moe, E.
• Funding Organization(s): The Research Council of Norway

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 

Literature

Crystal structure of the DNA polymerase III beta subunit ( beta-clamp) from the extremophile Deinococcus radiodurans.

Niiranen, L., Lian, K., Johnson, K.A., Moe, E.

(2015) BMC Struct Biol 15: 5-5

• PubMed: 25886944 
• DOI: https://doi.org/10.1186/s12900-015-0032-6
• Primary Citation of Related Structures:  
  4TRT


• PubMed Abstract: 
  

  Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans β-clamp (Drβ-clamp) at 2.0 Å resolution.

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Organizational Affiliation: 

The Norwegian Structural Biology Center (NorStruct), Department of Chemistry, UIT - the Arctic University of Norway, N-9037, Tromsø, Norway. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 79.09 kDa 
• Atom Count: 5,758 
• Modelled Residue Count: 722 
• Deposited Residue Count: 736 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase III subunit beta	A, B	368	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0  Gene Names: DR_0001 EC: 2.7.7.7
UniProt
Find proteins for Q9RYE8 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RYE8  Go to UniProtKB:  Q9RYE8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.198 
• R-Value Observed: 0.200 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.41	α = 90
b = 84.41	β = 90
c = 198.74	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
XSCALE	data scaling
XSCALE	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-04-29 
Deposition Author(s): Niiranen, L., Lian, K., Johnson, K.A., Moe, E.

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Funding Organization	Location	Grant Number
The Research Council of Norway	Norway	--

Revision History  

• Version 1.0: 2015-04-29
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Refinement description