Biological Assembly 1  

 3D View: Structure | Electron Density

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 43.89 kDa 
• Atom Count: 3262 
• Residue Count: 304 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

1PT3

Crystal structures of nuclease-ColE7 complexed with octamer DNA

• DOI: 10.2210/pdb1PT3/pdb
• NDB: PD0454

• Classification: Hydrolase/DNA
• Organism(s): Escherichia coli str. K-12 substr. W3110
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-22 Released: 2004-03-30 
• Deposition Author(s): Hsia, K.C., Chak, K.F., Cheng, Y.S., Ku, W.Y., Yuan, H.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.289 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 

Literature

DNA binding and degradation by the HNH protein ColE7.

Hsia, K.C., Chak, K.F., Liang, P.H., Cheng, Y.S., Ku, W.Y., Yuan, H.S.

(2004) Structure 12: 205-214

• PubMed: 14962381 
• DOI: 10.1016/j.str.2004.01.004
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The bacterial toxin ColE7 bears an HNH motif which has been identified in hundreds of prokaryotic and eukaryotic endonucleases, involved in DNA homing, restriction, repair, or chromosome degradation. The crystal structure of the nuclease domain of ColE7 in complex with a duplex DNA has been determined at 2.5 A resolution. The HNH motif is bound at the minor groove primarily to DNA phosphate groups at and beyond the 3' side of the scissile phosphate, with little interaction with ribose groups and bases. This result provides a structural basis for sugar- and sequence-independent DNA recognition and the inhibition mechanism by inhibitor Im7, which blocks the substrate binding site but not the active site. Structural comparison shows that two families of endonucleases bind and bend DNA in a similar way to that of the HNH ColE7, indicating that endonucleases containing a "betabetaalpha-metal" fold of active site possess a universal mode for protein-DNA interactions.

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Organizational Affiliation: 

Institute of Molecular Biology, National Yang-Ming University, Taipei, Taiwan.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Colicin E7	A, B	128	Escherichia coli str. K-12 substr. W3110	Mutation(s): 0  Gene Names: colE7 EC: 3.1
Find proteins for Q47112 (Escherichia coli) Explore Q47112  Go to UniProtKB:  Q47112

Entity ID: 1
Molecule	Chains	Length	Organism
5'-GCGATCGC-3'	C, D, E, F, G, H	8	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.289 
• R-Value Work: 0.216 
• R-Value Observed: 0.216 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.43	α = 90
b = 46.47	β = 90.39
c = 78.45	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-06-22 
• Released Date: 2004-03-30 
Deposition Author(s): Hsia, K.C., Chak, K.F., Cheng, Y.S., Ku, W.Y., Yuan, H.S.

Revision History 

• Version 1.0: 2004-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance