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), 0.286 (DCC)
R-Value Work:
0.235 (Depositor), 0.235 (DCC)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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), 0.286 (DCC)
R-Value Work: 0.235 (Depositor), 0.235 (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

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View more in-depth experimental data

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

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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.