7WT6 | pdb_00007wt6

Crystal structure of full-length peptidyl-tRNA hydrolase from Mycobacterium tuberculosis

PDB DOI: https://doi.org/10.2210/pdb7WT6/pdb

Classification: HYDROLASE
Organism(s): Mycobacteriaceae bacterium
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-02-04 Released: 2022-04-13
Deposition Author(s): Kulandaisamy, R., Das, U., Inampudi, K.K.
Funding Organization(s): Department of Science & Technology (DST, India), Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.94 Å
R-Value Free:
0.214 (Depositor), 0.213 (DCC)
R-Value Work:
0.169 (Depositor), 0.171 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of full-length peptidyl-tRNA hydrolase from Mycobacterium tuberculosis

Kulandaisamy, R., Das, U., Inampudi, K.K.

To be published.

Macromolecule Content

Total Structure Weight: 21.8 kDa
Atom Count: 1,645
Modeled Residue Count: 189
Deposited Residue Count: 202
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	202	Mycobacteriaceae bacterium	Mutation(s): 0 Gene Names: pth 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: 1.94 Å
R-Value Free: 0.214 (Depositor), 0.213 (DCC)
R-Value Work: 0.169 (Depositor), 0.171 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.581	α = 90
b = 39.003	β = 90
c = 123.818	γ = 90

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-04-13

Deposition Author(s):

Kulandaisamy, R.

Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	EEQ/2016/000507
Department of Biotechnology (DBT, India)	India	BT/PR34319/Med/29/1488/2019

Revision History (Full details and data files)

Version 1.0: 2022-04-13
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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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.