8XHR

Crystal structure of Mycobacterium tuberculosis MenT3 bound with CTP

PDB DOI: https://doi.org/10.2210/pdb8XHR/pdb

Classification: TRANSFERASE
Organism(s): Mycobacterium tuberculosis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-12-18 Released: 2024-02-28
Deposition Author(s): Liu, J., Yashiro, Y., Tomita, K.
Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.241
R-Value Work: 0.188
R-Value Observed: 0.191

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Substrate specificity of Mycobacterium tuberculosis terminal nucleotidyltransferase toxin MenT3

Liu, J., Yashiro, Y., Sakaguchi, Y., Suzuki, T., Tomita, K.

To be published.

Macromolecule Content

Total Structure Weight: 100.62 kDa
Atom Count: 7,061
Modelled Residue Count: 864
Deposited Residue Count: 903
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotidyl transferase AbiEii/AbiGii toxin family protein	A, B, C	301	Mycobacterium tuberculosis	Mutation(s): 1 Gene Names: Rv1045
UniProt
Find proteins for P96356 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P96356 Go to UniProtKB: P96356
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P96356
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CTP (Subject of Investigation/LOI) Query on CTP Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth B] SDF format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain E [auth B] MOL2 format, chain F [auth C]	D [auth A], E [auth B], F [auth C]	CYTIDINE-5'-TRIPHOSPHATE C₉ H₁₆ N₃ O₁₄ P₃ PCDQPRRSZKQHHS-XVFCMESISA-N		Interactions Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth B] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.241
R-Value Work: 0.188
R-Value Observed: 0.191
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.96	α = 90
b = 91.53	β = 101
c = 85.06	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-02-28

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H03980
Japan Society for the Promotion of Science (JSPS)	Japan	23H00368

Revision History (Full details and data files)

Version 1.0: 2024-02-28
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.