2QXF | pdb_00002qxf

Product bound structure of exonuclease I at 1.5 angstrom resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 
    0.224 (Depositor), 0.238 (DCC) 
  • R-Value Work: 
    0.199 (Depositor) 
  • R-Value Observed: 
    0.200 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history. 

Literature

Structure of Escherichia coli exonuclease I in complex with thymidine 5'-monophosphate.

Busam, R.D.

(2008) Acta Crystallogr D Biol Crystallogr 64: 206-210

  • DOI: https://doi.org/10.1107/S090744490706012X
  • Primary Citation Related Structures: 
    2QXF

  • PubMed Abstract: 

    In Escherichia coli, exonuclease I (ExoI) is a monomeric processive 3'-5' exonuclease that degrades single-stranded DNA. The enzyme has been implicated as primarily being involved in repairing frameshift mutations. The structure of the enzyme has previously been determined in a hexagonal space group at 2.4 A resolution. Here, the structure of ExoI in complex with a nucleotide product, thymidine 5'-monophosphate, is described in an orthorhombic space group at 1.5 A resolution. This new high-resolution structure provides some insight into the interactions involved in binding a nucleotide product. The conserved active site contains a unique metal-binding position when compared with orthologous sites in the Klenow fragment, T4 DNA polymerase and dnaQ. This unique difference is proposed to be a consequence of the repositioning of an important histidine, His181, away from the active site.

    • Organizational Affiliation: 
    • Institute of Molecular Biology, Howard Hughes Medical Institute and Department of Physics, 1229 University of Oregon, Eugene, OR 97403-1229, USA. robert.busam@ki.se

Macromolecule Content 

  • Total Structure Weight: 55.9 kDa 
  • Atom Count: 4,290 
  • Modeled Residue Count: 433 
  • Deposited Residue Count: 482 
  • Unique protein chains: 1

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Exodeoxyribonuclease I482Escherichia coli K-12Mutation(s): 0 
Gene Names: sbcB, cpeA, xonA, b2011, JW1993
EC: 3.1.11.1
UniProt
Find proteins for P04995 (Escherichia coli (strain K12))
Explore P04995 
Go to UniProtKB:  P04995
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04995
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free:  0.224 (Depositor), 0.238 (DCC) 
  • R-Value Work:  0.199 (Depositor) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.63α = 90
b = 91.849β = 90
c = 102.752γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
REFMACrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2008-01-22 
    • Deposition Author(s): Busam, R.D.

Revision History  (Full details and data files)

  • Version 1.0: 2008-01-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Source and taxonomy, Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations