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

wwPDB Validation 3D Report Full Report

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

Literature

Structural ans functional study of RNase J from Mycobacterium tuberculosis

Li, J., Hu, J., Bao, L., Zhan, B.

To be published.

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

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.