Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 21.60 kDa 
• Atom Count: 1057 
• Modelled Residue Count: 110 
• Deposited Residue Count: 186 
• Unique protein chains: 1

3PLW

Ref protein from P1 bacteriophage

• PDB DOI: 10.2210/pdb3PLW/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia virus P1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-11-15 Released: 2010-12-29 
• Deposition Author(s): Keck, J.L., Lu, D., Cox, M.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.172 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

Creating Directed Double-strand Breaks with the Ref Protein: A NOVEL RecA-DEPENDENT NUCLEASE FROM BACTERIOPHAGE P1.

Gruenig, M.C., Lu, D., Won, S.J., Dulberger, C.L., Manlick, A.J., Keck, J.L., Cox, M.M.

(2011) J Biol Chem 286: 8240-8251

• PubMed: 21193392 
• DOI: 10.1074/jbc.M110.205088
• Primary Citation of Related Structures:  
  3PLW


• PubMed Abstract: 
  

The bacteriophage P1-encoded Ref protein enhances RecA-dependent recombination in vivo by an unknown mechanism. We demonstrate that Ref is a new type of enzyme; that is, a RecA-dependent nuclease. Ref binds to ss- and dsDNA but does not cleave any DNA substrate until RecA protein and ATP are added to form RecA nucleoprotein filaments. Ref cleaves only where RecA protein is bound. RecA functions as a co-nuclease in the Ref/RecA system. Ref nuclease activity can be limited to the targeted strands of short RecA-containing D-loops. The result is a uniquely programmable endonuclease activity, producing targeted double-strand breaks at any chosen DNA sequence in an oligonucleotide-directed fashion. We present evidence indicating that cleavage occurs in the RecA filament groove. The structure of the Ref protein has been determined to 1.4 Å resolution. The core structure, consisting of residues 77-186, consists of a central 2-stranded β-hairpin that is sandwiched between several α-helical and extended loop elements. The N-terminal 76 amino acid residues are disordered; this flexible region is required for optimal activity. The overall structure of Ref, including several putative active site histidine residues, defines a new subclass of HNH-family nucleases. We propose that enhancement of recombination by Ref reflects the introduction of directed, recombinogenic double-strand breaks.

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Organizational Affiliation: 

Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Recombination enhancement function protein	A	186	Escherichia virus P1	Mutation(s): 0  Gene Names: ref
UniProt
Find proteins for P35926 (Escherichia phage P1) Explore P35926  Go to UniProtKB:  P35926

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.172 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.733	α = 90
b = 71.733	β = 90
c = 54.236	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-11-15 
• Released Date: 2010-12-29 
Deposition Author(s): Keck, J.L., Lu, D., Cox, M.M.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2018-02-07
  Changes: Experimental preparation