Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 163720.33 
• Atom Count: 9178 
• Residue Count: 1356 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2FDC

Structural Basis of DNA Damage Recognition and Processing by UvrB: crystal structure of a UvrB/DNA complex

• DOI: 10.2210/pdb2FDC/pdb
• NDB: PD0766

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Bacillus caldotenax
• Expression System: Escherichia coli


• Deposited: 2005-12-13 Released: 2006-03-14 
• Deposition Author(s): Truglio, J.J., Kisker, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.3 Å
• R-Value Free: 0.258 
• R-Value Work: 0.205 

Literature

Structural basis for DNA recognition and processing by UvrB.

Truglio, J.J., Karakas, E., Rhau, B., Wang, H., DellaVecchia, M.J., Van Houten, B., Kisker, C.

(2006) Nat.Struct.Mol.Biol. 13: 360-364

• PubMed: 16532007 
• DOI: 10.1038/nsmb1072


• PubMed Abstract: 
  

DNA-damage recognition in the nucleotide excision repair (NER) cascade is a complex process, operating on a wide variety of damages. UvrB is the central component in prokaryotic NER, directly involved in DNA-damage recognition and guiding the DNA through repair synthesis. We report the first structure of a UvrB-double-stranded DNA complex, providing insights into the mechanism by which UvrB binds DNA, leading to formation of the preincision complex. One DNA strand, containing a 3' overhang, threads behind a beta-hairpin motif of UvrB, indicating that this motif inserts between the strands of the double helix, thereby locking down either the damaged or undamaged strand. The nucleotide directly behind the beta-hairpin is flipped out and inserted into a small, highly conserved pocket in UvrB.

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Organizational Affiliation: 

Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York 11794-5115, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
UvrABC system protein B	A, B	658	Bacillus caldotenax	Mutation(s): 0  Gene Names: uvrB
Find proteins for P56981 (Bacillus caldotenax) Go to UniProtKB:  P56981

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(P*CP*GP*GP*CP*TP*CP*CP*AP*TP*CP*TP*CP*TP*AP*CP*CP*GP*CP*AP*A)-3'	C,D	20	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FLQ	C	N-[6-(ACETYLAMINO)HEXYL]-3',6'-DIHYDROXY-3-OXO-3H-SPIRO[2-BENZOFURAN-1,9'-XANTHENE]-6-CARBOXAMIDE FLUORESCEIN ADDUCT C29 H28 N2 O7 NYDPRVGMTFCAQC-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.3 Å
• R-Value Free: 0.258 
• R-Value Work: 0.205 
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 153.265	α = 90.00
b = 153.265	β = 90.00
c = 160.170	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-13 
• Released Date: 2006-03-14 
• Deposition Author(s): Truglio, J.J., Kisker, C.

Revision History 

• Version 1.0: 2006-03-14
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Version format compliance
• Version 1.3: 2017-10-18
  Type: Refinement description