9GP8

Crystal Structure of TgoT_PGLVVWA XNA Polymerase (Apo)

• PDB DOI: https://doi.org/10.2210/pdb9GP8/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Thermococcus gorgonarius
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-07 Released: 2024-10-02 
• Deposition Author(s): Dasoondi, R.S., Bellini, D., Holliger, P.
• Funding Organization(s): Medical Research Council (MRC, United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.282 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Starting Model: experimental

Literature

Crystal Structure of TgoT_PGLVVWA XNA Polymerase (Apo)

Dasoondi, R.S., Bellini, D., Holliger, P., Duffy, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 89.91 kDa 
• Atom Count: 6,598 
• Modelled Residue Count: 759 
• Deposited Residue Count: 773 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	773	Thermococcus gorgonarius	Mutation(s): 0  Gene Names: pol, polA EC: 2.7.7.7
UniProt
Find proteins for P56689 (Thermococcus gorgonarius) Explore P56689  Go to UniProtKB:  P56689

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.282 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.199	α = 90
b = 105.801	β = 90
c = 156.712	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Dasoondi, R.S., Bellini, D., Holliger, P.

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Funding Organization	Location	Grant Number
Medical Research Council (MRC, United Kingdom)	United Kingdom	--

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary