1FZR | pdb_00001fzr

CRYSTAL STRUCTURE OF BACTERIOPHAGE T7 ENDONUCLEASE I

• PDB DOI: https://doi.org/10.2210/pdb1FZR/pdb

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


• Deposited: 2000-10-04 Released: 2001-01-17 
• Deposition Author(s): Hadden, J.M., Convery, M.A., Declais, A.C., Lilley, D.M.J., Phillips, S.E.V.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Literature

Crystal structure of the Holliday junction resolving enzyme T7 endonuclease I.

Hadden, J.M., Convery, M.A., Declais, A.C., Lilley, D.M., Phillips, S.E.

(2001) Nat Struct Biol 8: 62-67

• PubMed: 11135673 
• DOI: https://doi.org/10.1038/83067
• Primary Citation Related Structures: 
  1FZR


• PubMed Abstract: 
  

  We have solved the crystal structure of the Holliday junction resolving enzyme T7 endonuclease I at 2.1 A resolution using the multiwavelength anomalous dispersion (MAD) technique. Endonuclease I exhibits strong structural specificity for four-way DNA junctions. The structure shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site. While no significant structural similarity could be detected with any other junction resolving enzyme, the active site is similar to that found in several restriction endonucleases. T7 endonuclease I therefore represents the first crystal structure of a junction resolving enzyme that is a member of the nuclease superfamily of enzymes.

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Organizational Affiliation: 
• Astbury Centre for Structural Molecular Biology, School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.

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: 64.28 kDa 
• Atom Count: 4,702 
• Modeled Residue Count: 516 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENDONUCLEASE I	A, B, C, D	138	Escherichia phage T7	Mutation(s): 1  EC: 3.1.21.2
UniProt
Find proteins for P00641 (Escherichia phage T7) Explore P00641  Go to UniProtKB:  P00641

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 123.66	α = 90
b = 135.19	β = 90
c = 61.58	γ = 90

Software Package:

Software Name	Purpose
SOLVE	phasing
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2001-01-17 
Deposition Author(s): Hadden, J.M., Convery, M.A., Declais, A.C., Lilley, D.M.J., Phillips, S.E.V.

Revision History  

• Version 1.0: 2001-01-17
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2024-02-07
  Changes: Data collection