7WNT

RNase J from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb7WNT/pdb

Classification: RNA BINDING PROTEIN
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-01-19 Released: 2023-01-25
Deposition Author(s): Li, J., Bao, L., Hu, J., Zhan, B., Li, Z.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.251
R-Value Work: 0.219
R-Value Observed: 0.221

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structural insights into RNase J that plays an essential role in Mycobacterium tuberculosis RNA metabolism

Bao, L., Hu, J., Zhan, B., Chi, M., Li, Z., Wang, S., Shan, C., Zhao, Z., Guo, Y., Ding, X., Ji, C., Tao, S., Ni, T., Zhang, X., Zhao, G., Li, J.

(2023) Nat Commun 14: 2280

DOI: https://doi.org/10.1038/s41467-023-38045-z

Macromolecule Content

Total Structure Weight: 59.73 kDa
Atom Count: 3,970
Modelled Residue Count: 529
Deposited Residue Count: 558
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease J	A	558	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: rnj EC: 3.1 (PDB Primary Data), 3.5.2.6 (PDB Primary Data)
UniProt
Find proteins for P9WGZ9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WGZ9 Go to UniProtKB: P9WGZ9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P9WGZ9
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		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: 2.44 Å
R-Value Free: 0.251
R-Value Work: 0.219
R-Value Observed: 0.221
Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.52	α = 90
b = 128.52	β = 90
c = 184.276	γ = 120

Software Package:

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

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2016YFA0500600

Revision History (Full details and data files)

Version 1.0: 2023-01-25
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description
Version 1.2: 2024-09-04
Changes: Database references

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 R01GM133198.