2V1C | pdb_00002v1c

Crystal structure and mutational study of RecOR provide insight into its role in DNA repair

• PDB DOI: https://doi.org/10.2210/pdb2V1C/pdb

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


• Deposited: 2007-05-23 Released: 2007-07-03 
• Deposition Author(s): Timmins, J., Leiros, I., McSweeney, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 
  0.443 (Depositor), 0.446 (DCC) 
• R-Value Work: 
  0.459 (Depositor), 0.428 (DCC) 
• R-Value Observed: 
  0.458 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure and Mutational Study of Recor Provide Insight Into its Mode of DNA Binding.

Timmins, J., Leiros, I., Mcsweeney, S.

(2007) EMBO J 26: 3260

• PubMed: 17581636 
• DOI: https://doi.org/10.1038/sj.emboj.7601760
• Primary Citation Related Structures: 
  2V1C


• PubMed Abstract: 
  

  The crystal structure of the complex formed between Deinococcus radiodurans RecR and RecO (drRecOR) has been determined. In accordance with previous biochemical characterisation, the drRecOR complex displays a RecR:RecO molecular ratio of 2:1. The biologically relevant drRecOR entity consists of a heterohexamer in the form of two drRecO molecules positioned on either side of the tetrameric ring of drRecR, with their OB (oligonucleotide/oligosaccharide-binding) domains pointing towards the interior of the ring. Mutagenesis studies validated the protein-protein interactions observed in the crystal structure and allowed mapping of the residues in the drRecOR complex required for DNA binding. Furthermore, the preferred DNA substrate of drRecOR was identified as being 3'-overhanging DNA, as encountered at ssDNA-dsDNA junctions. Together these results suggest a possible mechanism for drRecOR recognition of stalled replication forks.

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Organizational Affiliation: 
• Macromolecular Crystallography Group, European Synchrotron Radiation Facility, Grenoble-CEDEX 9, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A4B2 

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

Macromolecule Content 

• Total Structure Weight: 74.08 kDa 
• Atom Count: 4,781 
• Modeled Residue Count: 627 
• Deposited Residue Count: 684 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RECOMBINATION PROTEIN RECR	A, B	220	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0
UniProt
Find proteins for Q9ZNA2 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9ZNA2  Go to UniProtKB:  Q9ZNA2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HYPOTHETICAL PROTEIN	C	244	Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539	Mutation(s): 0
UniProt
Find proteins for Q9RW50 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RW50  Go to UniProtKB:  Q9RW50

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth B], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free:  0.443 (Depositor), 0.446 (DCC) 
• R-Value Work:  0.459 (Depositor), 0.428 (DCC) 
• R-Value Observed: 0.458 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144	α = 90
b = 83.2	β = 106.9
c = 66.6	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-03 
Deposition Author(s): Timmins, J., Leiros, I., McSweeney, S.

Revision History  

• Version 1.0: 2007-07-03
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description