6VF3

DNA Polymerase Mu, 8-oxorGTP:At Ground State Ternary Complex, 50 mM Mn2+ (15 min)

• PDB DOI: https://doi.org/10.2210/pdb6VF3/pdb
• NAKB: 6VF3

• Classification: REPLICATION
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-01-03 Released: 2021-09-01 
• Deposition Author(s): Jamsen, J.A., Wilson, S.H.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.180 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 

Literature

DNA Polymerase Mu, 8-oxorGTP:At Ground State Ternary Complex, 50 mM Mn2+ (15 min)

Jamsen, J.A., Sassa, A., Shock, D.D., Beard, W.A., Wilson, S.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: 46.76 kDa 
• Atom Count: 3,428 
• Modelled Residue Count: 343 
• Deposited Residue Count: 373 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed DNA/RNA polymerase mu	A	356	Homo sapiens	Mutation(s): 0  Gene Names: POLM, polmu EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP87 (Homo sapiens) Explore Q9NP87  Go to UniProtKB:  Q9NP87
PHAROS:  Q9NP87 GTEx:  ENSG00000122678

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')	B [auth T]	9	synthetic construct

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

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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8GT (Subject of Investigation/LOI)	J [auth A]	8-OXO-GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O15 P3 JCHLKIQZUXYLPW-UMMCILCDSA-N
EPE	I [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
DTT	Q [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
EDO	E [auth A], F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN (Subject of Investigation/LOI)	K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], R [auth T], S [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.52 Å
• R-Value Free: 0.180 
• R-Value Work: 0.163 
• R-Value Observed: 0.164 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.198	α = 90
b = 62.385	β = 90
c = 118.58	γ = 90

Software Package:

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

Structure Validation

Currently 6VF3 does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2021-09-01 
Deposition Author(s): Jamsen, J.A., Wilson, S.H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	Z01-ES050158
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	Z01-10ES050161
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	1K99ES029572-01
Japan Society for the Promotion of Science (JSPS)	Japan	16K16195

Revision History  

• Version 1.0: 2021-09-01
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Refinement description