8IU6

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)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.235 

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.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	186	Enterococcus faecium	Mutation(s): 1  Gene Names: pth
UniProt
Find proteins for A0A133CPV0 (Enterococcus faecium) Explore A0A133CPV0  Go to UniProtKB:  A0A133CPV0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.286 
• R-Value Work: 0.235 
• 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

Entry History & Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Pandey, R., Tripathi, S., Lanka, A.K., Zohib, M., 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
Department of Biotechnology (DBT, India)	India	BT/PR31893/MED/29/1390/2019

Revision History  

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