4G3I

Crystal structure of Dpo4 in complex with DNA duplex

• PDB DOI: https://doi.org/10.2210/pdb4G3I/pdb
• NAKB: 4G3I

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


• Deposited: 2012-07-14 Released: 2013-08-07 
• Deposition Author(s): Yan, Y.Y., Gan, J.H., Huang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 

Literature

Crystal structure of Dpo4 in complex with DNA duplex

Yan, Y.Y., Gan, J.H., Huang, Z.

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 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: 95.91 kDa 
• Atom Count: 6,238 
• Modelled Residue Count: 719 
• Deposited Residue Count: 742 
• 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]	342	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	A [auth C], C [auth E]	16	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA	B [auth D], D [auth F]	13	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	G [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.294 
• R-Value Work: 0.241 
• R-Value Observed: 0.243 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.472	α = 75.4
b = 52.634	β = 80.35
c = 99.445	γ = 70.97

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-07 
Deposition Author(s): Yan, Y.Y., Gan, J.H., Huang, Z.

Revision History  

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description