3CFO | pdb_00003cfo

Triple Mutant APO structure

• PDB DOI: https://doi.org/10.2210/pdb3CFO/pdb

• Classification: TRANSFERASE
• 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: 2.60 Å
• R-Value Free: 
  0.235 (Depositor) 
• R-Value Work: 
  0.192 (Depositor) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

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: 106.08 kDa 
• Atom Count: 7,695 
• Modeled Residue Count: 906 
• Deposited Residue Count: 909 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GMP	F [auth A]	GUANOSINE C10 H13 N5 O5 NYHBQMYGNKIUIF-UUOKFMHZSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.235 (Depositor) 
• R-Value Work:  0.192 (Depositor) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 82.307	α = 90
b = 116.424	β = 90
c = 198.769	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: 2023-08-30
  Changes: Data collection, Refinement description