2OWL | pdb_00002owl

Crystal structure of E. coli RdgC

• PDB DOI: https://doi.org/10.2210/pdb2OWL/pdb

• Classification: RECOMBINATION
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2007-02-16 Released: 2007-03-20 
• Deposition Author(s): Briggs, G.S., McEwan, P.A., Yu, J., Moore, T., Emsley, J., Lloyd, R.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.326 (Depositor), 0.321 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Literature

Ring Structure of the Escherichia coli DNA-binding Protein RdgC Associated with Recombination and Replication Fork Repair.

Briggs, G.S., McEwan, P.A., Yu, J., Moore, T., Emsley, J., Lloyd, R.G.

(2007) J Biological Chem 282: 12353-12357

• PubMed: 17308310 
• DOI: https://doi.org/10.1074/jbc.C700023200
• Primary Citation Related Structures: 
  2OWL


• PubMed Abstract: 
  

  The DNA-binding protein, RdgC, is associated with recombination and replication fork repair in Escherichia coli and with the virulence-associated, pilin antigenic variation mediated by RecA and other recombination proteins in Neisseria species. We solved the structure of the E. coli protein and refined it to 2.4A. RdgC crystallizes as a dimer with a head-to-head, tail-to-tail organization forming a ring with a 30 A diameter hole at the center. The protein fold is unique and reminiscent of a horseshoe with twin gates closing the open end. The central hole is lined with positively charged residues and provides a highly plausible DNA binding channel consistent with the nonspecific mode of binding detected in vitro and with the ability of RdgC to modulate RecA function in vivo.

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Organizational Affiliation: 
• Institute of Genetics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH.

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: 69.37 kDa 
• Atom Count: 4,806 
• Modeled Residue Count: 603 
• Deposited Residue Count: 606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombination-associated protein rdgC	A, B	303	Escherichia coli	Mutation(s): 13  Gene Names: rdgC
UniProt
Find proteins for P36767 (Escherichia coli (strain K12)) Explore P36767  Go to UniProtKB:  P36767

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth A], D [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.326 (Depositor), 0.321 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.425	α = 90
b = 95.683	β = 90
c = 171.576	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-20 
Deposition Author(s): Briggs, G.S., McEwan, P.A., Yu, J., Moore, T., Emsley, J., Lloyd, R.G.

Revision History  

• Version 1.0: 2007-03-20
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary