3CFP | pdb_00003cfp

Structure of the replicating complex of a POL Alpha family DNA Polymerase, ternary complex 1

• PDB DOI: https://doi.org/10.2210/pdb3CFP/pdb
• NAKB: 3CFP

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


• Deposited: 2008-03-04 Released: 2009-03-10 
• Deposition Author(s): Wang, J., Klimenko, D., Wang, M., Steitz, T.A., Konigsberg, W.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.267 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Insights into base selectivity from the structures of an RB69 DNA Polymerase triple mutant

Klimenko, D., Wang, M., Steitz, T.A., 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: 115.88 kDa 
• Atom Count: 8,326 
• Modeled Residue Count: 933 
• Deposited Residue Count: 941 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	C [auth A]	909	N/A	Mutation(s): 3  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: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DAP*DCP*DAP*DGP*DGP*DTP*DAP*DAP*DGP*DCP*DAP*DGP*DTP*DCP*DCP*DGP*DCP*DG)-3')	A [auth T]	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*DGP*DCP*DGP*DGP*DAP*DCP*DTP*DGP*DCP*DTP*DTP*DAP*DCP*(DOC))-3')	B [auth P]	14	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	I [auth A]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
CA	D [auth A], E [auth A], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.267 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.726	α = 90
b = 117.281	β = 90
c = 126.813	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-03-10 
Deposition Author(s): Wang, J., Klimenko, D., Wang, M., Steitz, T.A., Konigsberg, W.H.

Revision History  

• Version 1.0: 2009-03-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.3: 2024-02-21
  Changes: Data collection