1AVQ | pdb_00001avq

TOROIDAL STRUCTURE OF LAMBDA EXONUCLEASE DETERMINED AT 2.4 ANGSTROMS

• PDB DOI: https://doi.org/10.2210/pdb1AVQ/pdb

• Classification: DEOXYRIBONUCLEASE
• Organism(s): Lambdavirus lambda
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.40 Å
• R-Value Work: 
  0.198 (Depositor), 0.193 (DCC) 

Literature

Toroidal structure of lambda-exonuclease.

Kovall, R., Matthews, B.W.

(1997) Science 277: 1824-1827

• PubMed: 9295273 
• DOI: https://doi.org/10.1126/science.277.5333.1824
• Primary Citation Related Structures: 
  1AVQ


• 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.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 79.02 kDa 
• Atom Count: 5,933 
• Modeled Residue Count: 681 
• Deposited Residue Count: 684 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LAMBDA EXONUCLEASE	A, B, C	228	Lambdavirus lambda	Mutation(s): 0  EC: 3.1.11.3
UniProt
Find proteins for P03697 (Escherichia phage lambda) Explore P03697  Go to UniProtKB:  P03697

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], F [auth B], H [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	E [auth A], G [auth B], I [auth C], J [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Work:  0.198 (Depositor), 0.193 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 156.7	α = 90
b = 156.7	β = 90
c = 131.7	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-17
  Changes: Data collection, Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations