1RPL | pdb_00001rpl

2.3 ANGSTROMS CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF DNA POLYMERASE BETA

• PDB DOI: https://doi.org/10.2210/pdb1RPL/pdb

• Classification: NUCLEOTIDYLTRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1994-10-25 Released: 1995-01-26 
• Deposition Author(s): Davies II, J.F., Almassy, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work: 
  0.220 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

2.3 A crystal structure of the catalytic domain of DNA polymerase beta.

Davies 2nd., J.F., Almassy, R.J., Hostomska, Z., Ferre, R.A., Hostomsky, Z.

(1994) Cell 76: 1123-1133

• PubMed: 8137427 
• DOI: https://doi.org/10.1016/0092-8674(94)90388-3
• Primary Citation Related Structures: 
  1RPL


• PubMed Abstract: 
  

  The crystal structure of the catalytic domain of rat DNA polymerase beta (pol beta) has been determined at 2.3 A resolution and refined to an R factor of 0.22. The mixed alpha/beta protein has three subdomains arranged in an overall U shape reminiscent of other polymerase structures. The folding topology of pol beta, however, is unique. Two divalent metals bind near three aspartic acid residues implicated in the catalytic activity. In the presence of Mn2+ and dTTP, interpretable electron density is seen for two metals and the triphosphate, but not the deoxythymidine moiety. The principal interaction of the triphosphate moiety is with the bound divalent metals.

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Organizational Affiliation: 
• Agouron Pharmaceuticals, Incorporated, San Diego, California 92121.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 29.15 kDa 
• Atom Count: 2,024 
• Modeled Residue Count: 241 
• Deposited Residue Count: 251 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA POLYMERASE BETA	A	251	Rattus norvegicus	Mutation(s): 0  EC: 2.7.7.7 (UniProt), 4.2.99.18 (UniProt), 4.2.99 (UniProt)
UniProt
Find proteins for P06766 (Rattus norvegicus) Explore P06766  Go to UniProtKB:  P06766

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Work:  0.220 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.8	α = 90
b = 63.4	β = 90
c = 38.7	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1995-01-26 
Deposition Author(s): Davies II, J.F., Almassy, R.J.

Revision History  

• Version 1.0: 1995-01-26
  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: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references