1S7Z

Structure of Ocr from Bacteriophage T7

• PDB DOI: https://doi.org/10.2210/pdb1S7Z/pdb

• Classification: GENE REGULATION
• Organism(s): Escherichia phage T7
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-01-30 Released: 2004-02-10 
• Deposition Author(s): Walkinshaw, M.D., Taylor, P., Sturrock, S.S., Atanasiu, C., Berg, T., Henderson, R.M., Edwardson, J.M., Dryden, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.239 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 

Literature

Structure of Ocr from Bacteriophage T7, a Protein that Mimics B-Form DNA

Walkinshaw, M.D., Taylor, P., Sturrock, S.S., Atanasiu, C., Berg, T., Henderson, R.M., Edwardson, J.M., Dryden, D.T.

(2002) Mol Cell 9: 187-194

• PubMed: 11804597 
• DOI: https://doi.org/10.1016/s1097-2765(02)00435-5
• Primary Citation of Related Structures:  
  1S7Z


• PubMed Abstract: 
  

  We have solved, by X-ray crystallography to a resolution of 1.8 A, the structure of a protein capable of mimicking approximately 20 base pairs of B-form DNA. This ocr protein, encoded by gene 0.3 of bacteriophage T7, mimics the size and shape of a bent DNA molecule and the arrangement of negative charges along the phosphate backbone of B-form DNA. We also demonstrate that ocr is an efficient inhibitor in vivo of all known families of the complex type I DNA restriction enzymes. Using atomic force microscopy, we have also observed that type I enzymes induce a bend in DNA of similar magnitude to the bend in the ocr molecule. This first structure of an antirestriction protein demonstrates the construction of structural mimetics of long segments of B-form DNA.

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Organizational Affiliation: 

Institute of Cell and Molecular Biology, The King's Buildings, University of Edinburgh, EH9 3JR, Edinburgh, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 14.5 kDa 
• Atom Count: 997 
• Modelled Residue Count: 106 
• Deposited Residue Count: 117 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gene 0.3 protein	A	117	Escherichia phage T7	Mutation(s): 6  Gene Names: 0.3
UniProt
Find proteins for P03775 (Escherichia phage T7) Explore P03775  Go to UniProtKB:  P03775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CS	B [auth A], C [auth A], D [auth A]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.83 Å
• R-Value Free: 0.239 
• R-Value Work: 0.170 
• R-Value Observed: 0.173 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.777	α = 90
b = 37.665	β = 98.42
c = 35.49	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-10 
Deposition Author(s): Walkinshaw, M.D., Taylor, P., Sturrock, S.S., Atanasiu, C., Berg, T., Henderson, R.M., Edwardson, J.M., Dryden, D.T.

Revision History  

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary