Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 68.23 kDa 
• Atom Count: 547 
• Residue Count: 546 
• Unique protein chains: 1

1DPI

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

• DOI: 10.2210/pdb1DPI/pdb

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1987-08-11 Released: 1987-10-16 
• Deposition Author(s): Beese, L., Ollis, D., Steitz, T.

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Experimental Data Snapshot

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

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

• PubMed: 3883192 
• 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 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE I KLENOW FRAGMENT	A	605	Escherichia coli	Mutation(s): 0  Gene Names: T7 EC: 2.7.7.7
Find proteins for P00582 (Escherichia coli (strain K12)) Explore P00582  Go to UniProtKB:  P00582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 102.9	α = 90
b = 102.9	β = 90
c = 85.8	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1987-08-11 
• Released Date: 1987-10-16 
Deposition Author(s): Beese, L., Ollis, D., Steitz, T.

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