3TCN | pdb_00003tcn

Crystal structures of Peptidyl-tRNA hydrolase from Mycobacterium tuberculosis - Form 2 grown in presence of Pentaglycine

PDB DOI: https://doi.org/10.2210/pdb3TCN/pdb

Classification: HYDROLASE
Organism(s): Mycobacterium tuberculosis H37Rv
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-08-09 Released: 2012-02-15
Deposition Author(s): Selvaraj, M., Ahmad, R., Varshney, U., Vijayan, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.228 (Depositor), 0.228 (DCC)
R-Value Work:
0.180 (Depositor), 0.180 (DCC)

wwPDB Validation 3D Report Full Report

Validation slider image for 3TCN

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

Literature

Structures of new crystal forms of Mycobacterium tuberculosis peptidyl-tRNA hydrolase and functionally important plasticity of the molecule

Selvaraj, M., Ahmad, R., Varshney, U., Vijayan, M.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 124-128

PubMed: 22297982 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309111052341
Primary Citation Related Structures:
3TCK, 3TCN, 3TD2, 3TD6

PubMed Abstract:
The X-ray structures of new crystal forms of peptidyl-tRNA hydrolase from M. tuberculosis reported here and the results of previous X-ray studies of the enzyme from different sources provide a picture of the functionally relevant plasticity of the protein molecule. The new X-ray results confirm the connection deduced previously between the closure of the lid at the peptide-binding site and the opening of the gate that separates the peptide-binding and tRNA-binding sites. The plasticity of the molecule indicated by X-ray structures is in general agreement with that deduced from the available solution NMR results. The correlation between the lid and the gate movements is not, however, observed in the NMR structure.

Organizational Affiliation

Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.

Macromolecule Content

Total Structure Weight: 40.97 kDa
Atom Count: 3,114
Modeled Residue Count: 371
Deposited Residue Count: 382
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	191	Mycobacterium tuberculosis H37Rv	Mutation(s): 0 Gene Names: MT1042, MTCY10G2.35, pth, Rv1014c EC: 3.1.1.29
UniProt
Find proteins for P9WHN7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WHN7 Go to UniProtKB: P9WHN7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WHN7
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.228 (Depositor), 0.228 (DCC)
R-Value Work: 0.180 (Depositor), 0.180 (DCC)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.74	α = 90
b = 73.47	β = 93.48
c = 59.95	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-02-15

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-02-15
Type: Initial release
Version 1.1: 2024-03-20
Changes: Data collection, Database references

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.