3V6K | pdb_00003v6k

Replication of N2,3-Ethenoguanine by DNA Polymerases

• PDB DOI: https://doi.org/10.2210/pdb3V6K/pdb
• NAKB: 3V6K

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


• Deposited: 2011-12-20 Released: 2012-04-25 
• Deposition Author(s): Zhao, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 
  0.303 (Depositor), 0.312 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.245 (DCC) 
• R-Value Observed: 
  0.234 (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 Related Structures: 
  3V6H, 3V6J, 3V6K

---

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: 94.8 kDa 
• Atom Count: 6,100 
• Modeled Residue Count: 723 
• Deposited Residue Count: 742 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	A, B [auth J]	347	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: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*AP*AP*GP*GP*AP*TP*TP*CP*(2DT))-3')	C [auth P], E [auth K]	10	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*CP*(EFG)P*GP*AP*AP*TP*CP*CP*TP*TP*C)-3')	D [auth B], F [auth M]	14	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	I [auth A], J [auth A], K [auth A], N [auth J], P [auth J], Q [auth J], R [auth J]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	G [auth A], H [auth A], M [auth J], O [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	L [auth A], S [auth J], T [auth P], U [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free:  0.303 (Depositor), 0.312 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.245 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.855	α = 90
b = 110.953	β = 102.7
c = 100.238	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