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.

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

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

Organizational Affiliation

Institute of Cell and Molecular Biology, The King's Buildings, University of Edinburgh, EH9 3JR, Edinburgh, United Kingdom. malcolm.walkinsahaw@ed.ac.uk

Macromolecule Content

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

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03775
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CS Query on CS Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	CESIUM ION Cs NCMHKCKGHRPLCM-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on 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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-02-10

Deposition Author(s):

Revision History (Full details and data files)

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