8IU6 | pdb_00008iu6

Crystal structure of peptidyl-tRNA hydrolase mutant from Enterococcus faecium

PDB DOI: https://doi.org/10.2210/pdb8IU6/pdb

Classification: HYDROLASE
Organism(s): Enterococcus faecium
Expression System: Escherichia coli BL21
Mutation(s): Yes

Deposited: 2023-03-23 Released: 2024-04-03
Deposition Author(s): Pandey, R., Tripathi, S., Lanka, A.K., Zohib, M., Pal, R.K., Arora, A.
Funding Organization(s): Council of Scientific & Industrial Research (CSIR), Department of Biotechnology (DBT, India)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.286 (Depositor), 0.290 (DCC)
R-Value Work:
0.235 (Depositor), 0.240 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of peptidyl-tRNA hydrolase mutant from Enterococcus faecium

Pandey, R., Tripathi, S., Lanka, A.K., Zohib, M., Pal, R.K., Arora, A.

To be published.

Macromolecule Content

Total Structure Weight: 41.99 kDa
Atom Count: 2,888
Modeled Residue Count: 372
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	186	Enterococcus faecium	Mutation(s): 1 Gene Names: pth EC: 3.1.1.29
UniProt
Find proteins for A0A133CPV0 (Enterococcus faecium) Explore A0A133CPV0 Go to UniProtKB: A0A133CPV0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A133CPV0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.286 (Depositor), 0.290 (DCC)
R-Value Work: 0.235 (Depositor), 0.240 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.739	α = 90
b = 49.435	β = 107.868
c = 65.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
HKL-2000	data reduction
MOLREP	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	CSIR FBR MLP 2029
Department of Biotechnology (DBT, India)	India	BT/PR31893/MED/29/1390/2019

Revision History (Full details and data files)

Version 1.0: 2024-04-03
Type: Initial release

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.