2XCP

TERNARY COMPLEX OF SULFOLOBUS SOLFATARICUS DPO4 DNA POLYMERASE, 7,8- DIHYDRO-8-OXODEOXYGUANINE MODIFIED DNA AND dCTP - MAGNESIUM FORM

• PDB DOI: https://doi.org/10.2210/pdb2XCP/pdb
• NAKB: 2XCP

• Classification: DNA/TRANSFERASE
• Organism(s): Saccharolobus solfataricus P2
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-04-24 Released: 2010-09-08 
• Deposition Author(s): Irimia, A., Egli, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Starting Model: experimental

Literature

Metal Ion Dependence of the Active Site Conformation of the Trans-Lesion DNA Polymerase Dpo4 from Sulfolobus Solfataricus

Irimia, A., Loukachevitch, L.V., Eoff, R.L., Guengerich, F.P., Egli, M.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1013

• PubMed: 20823515 
• DOI: https://doi.org/10.1107/S1744309110029374
• Primary Citation of Related Structures:  
  2XC9, 2XCA, 2XCP


• PubMed Abstract: 
  

  Crystal structures of a binary Mg2+-form Dpo4-DNA complex with 1,N2-etheno-dG in the template strand as well as of ternary Mg2+-form Dpo4-DNA-dCTP/dGTP complexes with 8-oxoG in the template strand have been determined. Comparison of their conformations and active-site geometries with those of the corresponding Ca2+-form complexes revealed that the DNA and polymerase undergo subtle changes as a result of the catalytically more active Mg2+ occupying both the A and B sites.

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Organizational Affiliation: 

Department of Biochemistry and Center in Molecular Toxicology, Vanderbilt University, Nashville, TN 37232, 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: 102.19 kDa 
• Atom Count: 7,158 
• Modelled Residue Count: 747 
• Deposited Residue Count: 778 
• 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	358	Saccharolobus solfataricus P2	Mutation(s): 0  Gene Names: DPO4 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
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP *TP*DOC)-3'	C [auth E], E [auth P]	13	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*TP*CP*AP*CP*8OGP*GP*AP*AP*TP*CP*CP *TP*TP*CP*CP*CP*CP*C)-3'	D [auth F], F [auth T]	18	N/A

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.268 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.757	α = 90
b = 100.429	β = 96.08
c = 105.873	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-08 
Deposition Author(s): Irimia, A., Egli, M.

Revision History  

• Version 1.0: 2010-09-08
  Type: Initial release
  
• Version 1.1: 2012-04-18
  Changes: Database references, Version format compliance
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description