Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content

• Total Structure Weight: 79018.52 
• Atom Count: 5517 
• Residue Count: 684 
• Unique protein chains: 1

1AVQ

TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS

• DOI: 10.2210/pdb1AVQ/pdb

• Classification: DEOXYRIBONUCLEASE
• Organism(s): Escherichia phage lambda
• Expression System: Escherichia coli


• Deposited: 1997-09-18 Released: 1998-03-18 
• Deposition Author(s): Kovall, R.A., Matthews, B.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Work: 0.198 

Literature

Toroidal structure of lambda-exonuclease.

Kovall, R., Matthews, B.W.

(1997) Science 277: 1824-1827

• PubMed: 9295273 


• PubMed Abstract: 
  

Structure determination at 2.4 angstrom resolution shows that lambda-exonuclease consists of three subunits that form a toroid. The central channel is funnel shaped, tapering from an inner diameter of about 30 angstroms at the wider end to 15 angstroms at the narrow end. This is adequate to accommodate the DNA substrate and thus provides a structural basis for the ability of the enzyme to sequentially hydrolyze thousands of nucleotides in a highly processive manner. The results also suggest the locations of the active sites and the constraints that limit cleavage to a single strand.

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Organizational Affiliation: 

Institute of Molecular Biology, Howard Hughes Medical Institute, and Department of Physics, University of Oregon, Eugene, OR 97403, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LAMBDA EXONUCLEASE	A, B, C	228	Escherichia phage lambda	Mutation(s): 0  Gene Names: exo (red-alpha, redX) EC: 3.1.11.3
Find proteins for P03697 (Escherichia phage lambda) Go to UniProtKB:  P03697

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	A, B, C	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	A, B, C	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.4 Å
• R-Value Work: 0.198 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 156.700	α = 90.00
b = 156.700	β = 90.00
c = 131.700	γ = 90.00

Software Package:

Software Name	Purpose
XTALVIEW	refinement
DENZO	data reduction
TNT	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-09-18 
• Released Date: 1998-03-18 
• Deposition Author(s): Kovall, R.A., Matthews, B.W.

Revision History 

• Version 1.0: 1998-03-18
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2019-07-17
  Type: Data collection, Refinement description