9GP8 | pdb_00009gp8

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free:
0.282 (Depositor), 0.278 (DCC)
R-Value Work:
0.228 (Depositor), 0.228 (DCC)
R-Value Observed:
0.231 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal Structure of TgoT_PGLVVWA XNA Polymerase (Apo)

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

To be published.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P56689
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A], C [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain B [auth A] Focus chain C [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.18 Å
R-Value Free: 0.282 (Depositor), 0.278 (DCC)
R-Value Work: 0.228 (Depositor), 0.228 (DCC)
R-Value Observed: 0.231 (Depositor)

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

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-10-02

Deposition Author(s):

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

Revision History (Full details and data files)

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.