7Y52

Crystal structure of peptidyl-tRNA hydrolase from Enterococcus faecium

• PDB DOI: https://doi.org/10.2210/pdb7Y52/pdb

• Classification: HYDROLASE
• Organism(s): Enterococcus faecium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-06-16 Released: 2024-01-17 
• Deposition Author(s): Pandey, R., Zohib, M., Mundra, S., Pal, R.K., Arora, A.
• Funding Organization(s): Council of Scientific & Industrial Research (CSIR)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Crystal structure of peptidyl-tRNA hydrolase from Enterococcus faecium

Pandey, R., Zohib, M., Mundra, S., Pal, R.K., Arora, A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.68 kDa 
• Atom Count: 3,275 
• Modelled Residue Count: 375 
• Deposited Residue Count: 378 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	189	Enterococcus faecium	Mutation(s): 0  Gene Names:  pth, AWT83_04625, B1P95_10305, B4W81_05720, BU194_13660, CQR37_02495, CUM68_14530, CUN04_03690, CUS10_01235, CWC53_08420, DKP91_06400, DPX29_13995, DTPHA_1404154, EB12_02316, EB44_02271, EFM1CSP_02645, FIU59_04850, GBM44_12820, GBM73_11110 EC: 3.1.1.29
UniProt
Find proteins for A0A133CPV0 (Enterococcus faecium) Explore A0A133CPV0  Go to UniProtKB:  A0A133CPV0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	F [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA	C [auth A], E [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.234 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.821	α = 90
b = 74.835	β = 104.851
c = 63.751	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-17 
Deposition Author(s): Pandey, R., Zohib, M., Mundra, S., Pal, R.K., Arora, A.

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Funding Organization	Location	Grant Number
Council of Scientific & Industrial Research (CSIR)	India	CSIR FBR MLP 2029

Revision History  

• Version 1.0: 2024-01-17
  Type: Initial release