1DPI

STRUCTURE OF LARGE FRAGMENT OF ESCHERICHIA COLI DNA POLYMERASE I COMPLEXED WITH D/TMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP.

Ollis, D.L.Brick, P.Hamlin, R.Xuong, N.G.Steitz, T.A.

(1985) Nature 313: 762-766

  • DOI: 10.1038/313762a0
  • Primary Citation of Related Structures:  
    1DPI

  • PubMed Abstract: 
  • The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine monophosphate. The most stri ...

    The 3.3-A resolution crystal structure of the large proteolytic fragment of Escherichia coli DNA polymerase I complexed with deoxythymidine monophosphate consists of two domains, the smaller of which binds zinc-deoxythymidine monophosphate. The most striking feature of the larger domain is a deep crevice of the appropriate size and shape for binding double-stranded B-DNA. A flexible subdomain may allow the enzyme to surround completely the DNA substrate, thereby allowing processive nucleotide polymerization without enzyme dissociation.


    Related Citations: 
    • Domain of E. Coli DNA Polymerase I Showing Sequence Homology to T7 DNA Polymerase
      Ollis, D.L., Kline, C., Steitz, T.A.
      (1985) Nature 313: 818
    • Crystallization and 7 Angstroms Resolution Electron Density Map of the Large Fragment of Escherichia Coli DNA Polymerase I
      Brick, P., Ollis, D., Steitz, T.A.
      (1983) J Mol Biol 166: 453
    • Nucleotide Sequence of the Escherichia Coli Pola Gene and Primary Structure of DNA Polymerase I
      Joyce, C.M., Kelley, W.S., Grindley, N.D.F.
      (1982) J Biol Chem 257: 1958
    • Escherichia Coli DNA Polymerase I. Sequence Characterization and Secondary Structure Prediction
      Brown, W.E., Stump, K.H., Kelley, W.S.
      (1982) J Biol Chem 257: 1965

    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA POLYMERASE I KLENOW FRAGMENT A605Escherichia coliMutation(s): 0 
Gene Names: T7
EC: 2.7.7.7
Find proteins for P00582 (Escherichia coli (strain K12))
Explore P00582 
Go to UniProtKB:  P00582
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Observed: 0.200 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.9α = 90
b = 102.9β = 90
c = 85.8γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1987-10-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance