4YMM | pdb_00004ymm

Structure of human DNA polymerase beta complexed with 7BG as the template base in a 1-nucleotide gapped DNA

• PDB DOI: https://doi.org/10.2210/pdb4YMM/pdb
• NAKB: 4YMM

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-06 Released: 2016-03-09 
• Deposition Author(s): Lee, S., Koag, M.-C.
• 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: 2.20 Å
• R-Value Free: 
  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Structure of human DNA polymerase beta complexed with 7BG as the template base in a 1-nucleotide gapped DNA

Lee, S., Koag, M.-C.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.86 kDa 
• Atom Count: 3,345 
• Modeled Residue Count: 358 
• Deposited Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	335	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 16-mer (template)	B [auth T]	16	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA 10-mer (up-primer)	C [auth P]	10	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA 5-mer (dn-primer)	D	5	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.257 (Depositor), 0.254 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.426	α = 90
b = 78.966	β = 106.34
c = 54.838	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-09 
Deposition Author(s): Lee, S., Koag, M.-C.

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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: 2016-03-09
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-18
  Changes: Author supporting evidence
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations