3QEX | pdb_00003qex

RB69 DNA Polymerase (L561A/S565G/Y567A) Ternary Complex with dGTP Opposite dT

• PDB DOI: https://doi.org/10.2210/pdb3QEX/pdb
• NAKB: 3QEX

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


• Deposited: 2011-01-20 Released: 2012-01-25 
• Deposition Author(s): Xia, S., Konigsberg, W.H., Wang, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 
  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Hydrogen-Bonding Capability of Difluorotoluene Nucleoside in Replication Complexes

Xia, S., Konigsberg, W.H., Wang, 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: 114.67 kDa 
• Atom Count: 9,070 
• 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): 5  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 (5'-D(*TP*CP*AP*TP*GP*TP*AP*AP*GP*CP*AP*GP*TP*CP*CP*GP*CP*G)-3')	B [auth T]	18	synthetic construct

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGT	D [auth A]	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 HAAZLUGHYHWQIW-KVQBGUIXSA-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: 1.73 Å
• R-Value Free:  0.206 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.991	α = 90
b = 120.211	β = 90
c = 130.361	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: 2012-01-25 
Deposition Author(s): Xia, S., Konigsberg, W.H., Wang, J.

Revision History  

• Version 1.0: 2012-01-25
  Type: Initial release
  
• Version 1.1: 2024-02-21
  Changes: Data collection, Database references, Derived calculations