3V6H | pdb_00003v6h

Replication of N2,3-Ethenoguanine by DNA Polymerases

• PDB DOI: https://doi.org/10.2210/pdb3V6H/pdb
• NAKB: 3V6H

• Classification: TRANSFERASE/DNA
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-12-19 Released: 2012-04-25 
• Deposition Author(s): Zhao, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

Replication of n(2) ,3-ethenoguanine by DNA polymerases.

Zhao, L., Christov, P.P., Kozekov, I.D., Pence, M.G., Pallan, P.S., Rizzo, C.J., Egli, M., Guengerich, F.P.

(2012) Angew Chem Int Ed Engl 51: 5466-5469

• PubMed: 22488769 
• DOI: https://doi.org/10.1002/anie.201109004
• Primary Citation of Related Structures:  
  3V6H, 3V6J, 3V6K

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Organizational Affiliation: 

Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University School of Medicine, Nashville, TN 37232-0146, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 100.1 kDa 
• Atom Count: 6,867 
• Modelled Residue Count: 738 
• Deposited Residue Count: 758 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	E [auth A], F [auth B]	348	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: dbh, dpo4, SSO2448 EC: 2.7.7.7
UniProt
Find proteins for Q97W02 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97W02  Go to UniProtKB:  Q97W02

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')	A [auth T], C	18	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*G*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*(DOC))-3')	B [auth P], D	13	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCP	H [auth A], L [auth B]	2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE C9 H16 N3 O13 P3 RGWHQCVHVJXOKC-SHYZEUOFSA-N
CA	G [auth D], K [auth A], N [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	I [auth A], J [auth A], M [auth B], O [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.267 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.532	α = 90
b = 111.267	β = 102.68
c = 98.942	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-25 
Deposition Author(s): Zhao, L.

Revision History  

• Version 1.0: 2012-04-25
  Type: Initial release
  
• Version 1.1: 2012-06-06
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description