9NKE | pdb_00009nke

Dpo4 DNA polymerase (R336A) in complex with DNA containing an 8oxoG template lesion

• PDB DOI: https://doi.org/10.2210/pdb9NKE/pdb
• NAKB: 9NKE

• Classification: TRANSFERASE/DNA
• Organism(s): Saccharolobus solfataricus P2, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2025-02-28 Released: 2025-09-24 
• Deposition Author(s): Pata, J.D., Liang, B.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Pinky-trigger residues in the Y-family Dpo4 DNA polymerase communicate to restrict downstream synthesis past 8-oxoguanine lesions

Disha, S.S., Punchipatabendi, T.I., Kaszubowski, J.D., Liang, B., Pata, J.D., Trakselis, M.A.

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)

Biological Assembly Evidence: homology

Biological Assembly 2  

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

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

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 100.25 kDa 
• Atom Count: 6,759 
• Modeled Residue Count: 741 
• Deposited Residue Count: 765 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	A, D [auth B]	352	Saccharolobus solfataricus P2	Mutation(s): 1  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
Extended Primer Strand	B [auth P]	14	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Template DNA	C [auth T], F [auth D]	17	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
Primer Strand	E [auth C]	13	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP (Subject of Investigation/LOI)	G [auth A], K [auth B]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
PO4	J [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA	H [auth A], I [auth A], L [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.273 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.199 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.309	α = 90
b = 103.575	β = 90
c = 105.842	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-09-24 
Deposition Author(s): Pata, J.D., Liang, B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM08057308
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R15GM155805

Revision History  

• Version 1.0: 2025-09-24
  Type: Initial release