1N48 | pdb_00001n48

Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion

• PDB DOI: https://doi.org/10.2210/pdb1N48/pdb
• NAKB: 1N48

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


• Deposited: 2002-10-30 Released: 2004-02-24 
• Deposition Author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.230 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

A Y-family polymerase complexed with abasic lesions: catching DNA with a loaded nucleoside triphosphate

Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.61 kDa 
• Atom Count: 3,782 
• Modeled Residue Count: 371 
• Deposited Residue Count: 381 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase IV	C [auth A]	352	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: 1
Molecule	Chains	Length	Organism	Image
5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*A)-3'	A [auth B]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*(3DR)P*TP*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'	B [auth C]	16	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth B]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CA	D [auth B], F [auth A], G [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.230 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.546	α = 90
b = 88.458	β = 90
c = 92.389	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-24 
Deposition Author(s): Ling, H., Boudsocq, F., Woodgate, R., Yang, W.

Revision History  

• Version 1.0: 2004-02-24
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description