4O6O | pdb_00004o6o

Structural and functional studies the characterization of Cys4 Zinc-finger motif in the recombination mediator protein RecR

• PDB DOI: https://doi.org/10.2210/pdb4O6O/pdb

• Classification: RECOMBINATION
• Organism(s): Caldanaerobacter subterraneus subsp. tengcongensis MB4
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-12-23 Released: 2014-12-10 
• Deposition Author(s): Tang, Q., Liu, Y.P., Yan, X.X., Liang, D.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 
  0.255 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.227 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of Cys4 zinc finger motif in the recombination mediator protein RecR.

Tang, Q., Liu, Y.P., Yan, X.X., Liang, D.C.

(2014) DNA Repair (Amst) 24: 10-14

• PubMed: 25460918 
• DOI: https://doi.org/10.1016/j.dnarep.2014.09.012
• Primary Citation Related Structures: 
  4O6O, 4O6P


• PubMed Abstract: 
  

  Zinc finger motif widely exists in protein structure, which can play different roles in different proteins. RecR is an important recombination mediator protein (RMP) in the RecFOR pathway and zinc finger motif is the most conserved domain in RecR protein. However, the function of this zinc finger motif in RecR is unclear. Here, we have studied the structures of the single cysteine and double cysteines mutation within the zinc finger motif in Thermoanaerobacter tengcongensis RecR (TTERecR). We have also studied the DNA binding ability as well as TTERecO protein binding ability of single, double and even triple cysteines mutation of the zinc finger motif, and the mutants do not alter DNA binding by RecR nor the interaction between RecR and RecO. The function of TTERecR zinc finger motif is to maintain the stability of the three-dimensional structure.

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Organizational Affiliation: 
• National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: [e-mail].
National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. Electronic address: [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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.83 kDa 
• Atom Count: 6,209 
• Modeled Residue Count: 790 
• Deposited Residue Count: 848 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombination protein RecR	A, B, C, D	212	Caldanaerobacter subterraneus subsp. tengcongensis MB4	Mutation(s): 1  Gene Names: recR
UniProt
Find proteins for Q8RDI4 (Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4)) Explore Q8RDI4  Go to UniProtKB:  Q8RDI4

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	F [auth A], G [auth A], I [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	E [auth A], H [auth B], J [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free:  0.255 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.227 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.604	α = 90
b = 67.912	β = 92.98
c = 94.364	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Tang, Q., Liu, Y.P., Yan, X.X., Liang, D.C.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description