4PHE | pdb_00004phe

Structure of human DNA polymerase beta complexed with T in the template base paired with incoming non-hydrolyzable GTP

• PDB DOI: https://doi.org/10.2210/pdb4PHE/pdb
• NAKB: 4PHE

• Classification: Transferase,Lyase/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Enterobacteria phage L1
• Mutation(s): No 


• Deposited: 2014-05-06 Released: 2015-05-06 
• Deposition Author(s): Koag, M.C., Lee, S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Literature

The spontaneous base substitution mechanisms of human DNA polymerase beta

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: 47.58 kDa 
• Atom Count: 3,388 
• Modeled Residue Count: 356 
• Deposited Residue Count: 360 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	329	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746  Go to UniProtKB:  P06746
PHAROS:  P06746 GTEx:  ENSG00000070501

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*AP*CP*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	B [auth T]	16	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3')	C [auth P]	10	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*CP*GP*G)-3')	D	5	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XG4	I [auth A]	2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine C10 H17 N6 O12 P3 DWGAAFQEGIMTIA-KVQBGUIXSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.535	α = 90
b = 79.093	β = 105.78
c = 54.796	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
REFMAC	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-05-06 
Deposition Author(s): Koag, M.C., Lee, S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES23101

Revision History  

• Version 1.0: 2015-05-06
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Refinement description