3V7K | pdb_00003v7k

Co-crystal structure of K72E variant of rat polymerase beta: Enzyme-DNA binary complex

• PDB DOI: https://doi.org/10.2210/pdb3V7K/pdb
• NAKB: 3V7K

• Classification: Transferase/DNA
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2011-12-21 Released: 2013-01-16 
• Deposition Author(s): Rangarajan, S., Jaeger, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 
  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.218 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Literature

Crystallographic studies of K72E mutant DNA polymerase explain loss of lyase function and reveal changes in the overall conformational state of the polymerase domain

Rangarajan, S., Gridley, C.L., Firbank, S., Dalal, S., Sweasy, J.B., Jaeger, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 44.93 kDa 
• Atom Count: 3,181 
• Modeled Residue Count: 350 
• Deposited Residue Count: 359 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	340	Rattus norvegicus	Mutation(s): 1  Gene Names: Polb EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt
Find proteins for P06766 (Rattus norvegicus) Explore P06766  Go to UniProtKB:  P06766

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*GP*TP*GP*AP*GP*T)-3')	B [auth P]	8	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*AP*AP*AP*CP*TP*CP*AP*CP*AP*A)-3')	C [auth T]	11	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth A], E [auth A], F [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free:  0.277 (Depositor), 0.273 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.218 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.464	α = 90
b = 75.508	β = 90
c = 117.359	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHENIX	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Rangarajan, S., Jaeger, J.

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.2: 2024-02-28
  Changes: Advisory, Data collection, Database references, Derived calculations