Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 114.74 kDa 
• Atom Count: 9332 
• Residue Count: 932 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

3QEP

RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dTTP Opposite Difluorotoluene Nucleoside

• DOI: 10.2210/pdb3QEP/pdb
• NDB: NA0953

• Classification: Transferase/DNA
• Organism(s): Escherichia phage RB69, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2011-01-20 Released: 2011-08-31 
• Deposition Author(s): Xia, S., Konigsberg, W.H., Wang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.204 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

Literature

Hydrogen-bonding capability of a templating difluorotoluene nucleotide residue in an RB69 DNA polymerase ternary complex.

Xia, S., Konigsberg, W.H., Wang, J.

(2011) J Am Chem Soc 133: 10003-10005

• PubMed: 21667997 
• DOI: 10.1021/ja2021735
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Results obtained using 2,4-difluorotoluene nucleobase (dF) as a nonpolar thymine isostere by Kool and colleagues challenged the Watson-Crick dogma that hydrogen bonds between complementary bases are an absolute requirement for accurate DNA replication. Here, we report crystal structure of an RB69 DNA polymerase L561A/S565G/Y567A triple mutant ternary complex with a templating dF opposite dTTP at 1.8 Å-resolution. In this structure, direct hydrogen bonds were observed between: (i) dF and the incoming dTTP, (ii) dF and residue G568 of the polymerase, and (iii) dF and ordered water molecules surrounding the nascent base pair. Therefore, this structure provides evidence that a templating dF can form novel hydrogen bonds with the incoming dTTP and with the enzyme that differ from those formed with a templating dT.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DNA polymerase	A	903	Escherichia phage RB69	Mutation(s): 3  Gene Names: 43 EC: 2.7.7.7 (PDB Primary Data), 3.1.11 (UniProt)
Find proteins for Q38087 (Escherichia phage RB69) Go to UniProtKB:  Q38087

Entity ID: 2
Molecule	Chains	Length	Organism
DNA (5'-D(*TP*CP*GP*(DFT)P*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')	T	18	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism
DNA (5'-D(*GP*CP*GP*GP*AP*CP*TP*GP*CP*TP*TP*AP*(DOC))-3')	P	13	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	A	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
CA	A, P	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.204 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.133	α = 90
b = 119.774	β = 90
c = 130.481	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

• Deposited Date: 2011-01-20 
• Released Date: 2011-08-31 
Deposition Author(s): Xia, S., Konigsberg, W.H., Wang, J.

Revision History 

• Version 1.0: 2011-08-31
  Type: Initial release