1DPI | pdb_00001dpi

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

• PDB DOI: https://doi.org/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 (Depositor) 

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: https://doi.org/10.1038/313762a0
• Primary Citation 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.

Biological Assembly 1  

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 
• Modeled Residue Count: 546 
• Deposited Residue Count: 605 
• Unique protein chains: 1

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
UniProt
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	B [auth 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 (Depositor) 

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

• 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
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Other