8T3X | pdb_00008t3x

TNA polymerase, closed ternary

• PDB DOI: https://doi.org/10.2210/pdb8T3X/pdb
• NAKB: 8T3X

• Classification: TRANSFERASE/DNA
• Organism(s): Thermococcus kodakarensis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2023-06-07 Released: 2024-08-28 
• Deposition Author(s): Maola, V., Chaput, J., Chim, N.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free: 
  0.301 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.242 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.247 (Depositor) 

Starting Model: experimental

Literature

Directed evolution of a highly efficient TNA polymerase achieved by homologous recombination

Maola, V.A., Yik, E.J., Hajjar, M., Lee, J.J., Holguin, M.J., Quijano, R.N., Nguyen, K.K., Ho, K.L., Medina, J.V., Chim, N., Chaput, J.C.

(2024) Nat Catal 

• DOI: https://doi.org/10.1038/s41929-024-01233-1

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: 97.42 kDa 
• Atom Count: 6,778 
• Modeled Residue Count: 775 
• Deposited Residue Count: 787 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
10-92, TNA polymerase	A	760	Thermococcus kodakarensis	Mutation(s): 51  EC: 2.7.7.7
UniProt
Find proteins for D0VWU9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore D0VWU9  Go to UniProtKB:  D0VWU9

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Template	B [auth T]	15	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
Primer	C [auth P]	12	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9O7	D [auth A]	[(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl] [oxidanyl(phosphonooxy)phosphoryl] hydrogen phosphate C9 H14 N5 O12 P3 AWDFERYZHFHVNT-AFEQZKEHSA-N
EPE	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.73 Å
• R-Value Free:  0.301 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.242 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.247 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.869	α = 90
b = 99.525	β = 90
c = 110.727	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-08-28 
Deposition Author(s): Maola, V., Chaput, J., Chim, N.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	--

Revision History  

• Version 1.0: 2024-08-28
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Database references, Structure summary