3FPN | pdb_00003fpn

Crystal structure of UvrA-UvrB interaction domains

• PDB DOI: https://doi.org/10.2210/pdb3FPN/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-05 Released: 2009-03-24 
• Deposition Author(s): Pakotiprapha, D., Verdine, G.L., Jeruzalmi, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.229 (DCC) 
• R-Value Observed: 
  0.231 (Depositor) 

Starting Models: experimental

Literature

A Structural Model for the Damage-sensing Complex in Bacterial Nucleotide Excision Repair.

Pakotiprapha, D., Liu, Y., Verdine, G.L., Jeruzalmi, D.

(2009) J Biological Chem 284: 12837-12844

• PubMed: 19287003 
• DOI: https://doi.org/10.1074/jbc.M900571200
• Primary Citation Related Structures: 
  3FPN


• PubMed Abstract: 
  

  Nucleotide excision repair is distinguished from other DNA repair pathways by its ability to process a wide range of structurally unrelated DNA lesions. In bacteria, damage recognition is achieved by the UvrA.UvrB ensemble. Here, we report the structure of the complex between the interaction domains of UvrA and UvrB. These domains are necessary and sufficient for full-length UvrA and UvrB to associate and thereby form the DNA damage-sensing complex of bacterial nucleotide excision repair. The crystal structure and accompanying biochemical analyses suggest a model for the complete damage-sensing complex.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.71 kDa 
• Atom Count: 1,757 
• Modeled Residue Count: 212 
• Deposited Residue Count: 225 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Geobacillus stearothermophilus UvrA interaction domain	A	119	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: uvrA
UniProt
Find proteins for D0VX13 (Geobacillus stearothermophilus) Explore D0VX13  Go to UniProtKB:  D0VX13

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Geobacillus stearothermophilus UvrB interaction domain	B	106	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: uvrB
UniProt
Find proteins for D0VX12 (Geobacillus stearothermophilus) Explore D0VX12  Go to UniProtKB:  D0VX12

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.229 (DCC) 
• R-Value Observed: 0.231 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.491	α = 90
b = 84.491	β = 90
c = 60.874	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-24 
Deposition Author(s): Pakotiprapha, D., Verdine, G.L., Jeruzalmi, D.

Revision History  

• Version 1.0: 2009-03-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description