4M3X

RB69 DNA polymerase ternary complex with dT/dG at position n-5 of primer/template duplex

• PDB DOI: https://doi.org/10.2210/pdb4M3X/pdb
• NAKB: 4M3X

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia phage RB69
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-08-06 Released: 2014-02-12 
• Deposition Author(s): Xia, S., Konigsberg, W.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 

Literature

Mispairs with Watson-Crick base-pair geometry observed in ternary complexes of an RB69 DNA polymerase variant.

Xia, S., Konigsberg, W.H.

(2014) Protein Sci 23: 508-513

• PubMed: 24458997 
• DOI: https://doi.org/10.1002/pro.2434
• Primary Citation of Related Structures:  
  4M3R, 4M3T, 4M3U, 4M3W, 4M3X, 4M3Y, 4M3Z, 4M41, 4M42, 4M45


• PubMed Abstract: 
  

  Recent structures of DNA polymerase complexes with dGMPCPP/dT and dCTP/dA mispairs at the insertion site have shown that they adopt Watson-Crick geometry in the presence of Mn(2+) indicating that the tautomeric or ionization state of the base has changed. To see whether the tautomeric or ionization state of base-pair could be affected by its microenvironment, we determined 10 structures of an RB69 DNA polymerase quadruple mutant with dG/dT or dT/dG mispairs at position n-1 to n-5 of the Primer/Template duplex. Different shapes of the mispairs, including Watson-Crick geometry, have been observed, strongly suggesting that the local environment of base-pairs plays an important role in their tautomeric or ionization states.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, 06520-8114.

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: 114.67 kDa 
• Atom Count: 8,298 
• Modelled Residue Count: 932 
• Deposited Residue Count: 934 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	903	Escherichia phage RB69	Mutation(s): 6  Gene Names: 43 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
UniProt
Find proteins for Q38087 (Escherichia phage RB69) Explore Q38087  Go to UniProtKB:  Q38087

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA template	B [auth T]	18	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA primer	C [auth P]	13	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	D [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.241 
• R-Value Work: 0.191 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.118	α = 90
b = 119.82	β = 90
c = 130.266	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-12 
Deposition Author(s): Xia, S., Konigsberg, W.H.

Revision History  

• Version 1.0: 2014-02-12
  Type: Initial release
  
• Version 1.1: 2014-04-09
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations