5EDW | pdb_00005edw

Ternary structure of Dpo4 bound to G in the template base paired with incoming dTTP

• PDB DOI: https://doi.org/10.2210/pdb5EDW/pdb
• NAKB: 5EDW

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


• Deposited: 2015-10-22 Released: 2016-11-02 
• Deposition Author(s): Koag, M.-C., Lee, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free: 
  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Structure of Dpo4 DNA polymerase replicating across the genotoxic N7-methylguanine lesion

Koag, M.-C., Lee, S.

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: 49.42 kDa 
• Atom Count: 3,466 
• Modeled Residue Count: 373 
• Deposited Residue Count: 373 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	A	341	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(*CP*TP*AP*AP*CP*GP*GP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')	B [auth T]	19	Saccharolobus solfataricus P2

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3')	C [auth P]	13	Saccharolobus solfataricus P2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	G [auth A]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
CA	D [auth A], E [auth A], F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.62 Å
• R-Value Free:  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.516	α = 90
b = 101.994	β = 90
c = 52.864	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-02 
Deposition Author(s): Koag, M.-C., Lee, S.

Revision History  

• Version 1.0: 2016-11-02
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description