3Q8S | pdb_00003q8s

Human DNA polymerase iota incorporating dTTP opposite 8-oxo-guanine

• PDB DOI: https://doi.org/10.2210/pdb3Q8S/pdb
• NAKB: 3Q8S

• Classification: Transferase/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-06 Released: 2011-02-23 
• Deposition Author(s): Kirouac, K.N., Ling, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free: 
  0.266 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Human DNA polymerase iota incorporating dTTP opposite 8-oxo-guanine

Kirouac, K.N., Ling, H.

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: 53.05 kDa 
• Atom Count: 3,581 
• Modeled Residue Count: 395 
• Deposited Residue Count: 438 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase iota	A [auth B]	420	Homo sapiens	Mutation(s): 0  Gene Names: POLI, RAD30B EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNA4 (Homo sapiens) Explore Q9UNA4  Go to UniProtKB:  Q9UNA4
PHAROS:  Q9UNA4 GTEx:  ENSG00000101751

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*AP*(8OG)P*GP*GP*GP*TP*CP*CP*T)-3')	B [auth T]	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*GP*AP*CP*CP*C)-3')	C [auth P]	7	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TTP	F [auth B]	THYMIDINE-5'-TRIPHOSPHATE C10 H17 N2 O14 P3 NHVNXKFIZYSCEB-XLPZGREQSA-N
MG	D [auth B], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Free:  0.266 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.494	α = 90
b = 97.494	β = 90
c = 201.899	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-23 
Deposition Author(s): Kirouac, K.N., Ling, H.

Revision History  

• Version 1.0: 2011-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-11-16
  Changes: Atomic model
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations