5EKT

Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from Vibrio cholerae at 1.63A resolution.

• PDB DOI: https://doi.org/10.2210/pdb5EKT/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O1 biovar El Tor str. N16961
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-11-04 Released: 2016-11-09 
• Deposition Author(s): Shahid, S., Kabr, A., Pal, R.K., Arora, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Crystal structure of mutant-K146A of peptidyl-tRNA hydrolase from Vibrio cholerae at 1.63A resolution.

Shahid, S., Kabra, A., 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 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 43.63 kDa 
• Atom Count: 3,430 
• Modelled Residue Count: 394 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	199	Vibrio cholerae O1 biovar El Tor str. N16961	Mutation(s): 1  Gene Names: pth, VC_2184 EC: 3.1.1.29
UniProt
Find proteins for Q9KQ21 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Explore Q9KQ21  Go to UniProtKB:  Q9KQ21

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth B]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
2CO	A, B	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.228 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.934	α = 90
b = 74.295	β = 90
c = 123.571	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Shahid, S., Kabr, A., Pal, R.K., Arora, A.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description