5GVZ | pdb_00005gvz

Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at resolution 1.75A.

• PDB DOI: https://doi.org/10.2210/pdb5GVZ/pdb

• Classification: HYDROLASE
• Organism(s): Vibrio cholerae O395
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-09-07 Released: 2017-09-20 
• Deposition Author(s): Shahid, S., Kabra, A., Pal, R.K., Arora, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of Peptidyl-tRNA hydrolase from Vibrio cholerae in space group C2221 at resolution 1.75A.

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.

Macromolecule Content 

• Total Structure Weight: 21.86 kDa 
• Atom Count: 1,634 
• Modeled Residue Count: 194 
• Deposited Residue Count: 197 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	197	Vibrio cholerae O395	Mutation(s): 0  Gene Names: pth, VC0395_A1761, VC395_2298 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	C [auth A], D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.235 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.136	α = 90
b = 73.462	β = 90
c = 120.52	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-09-20 
Deposition Author(s): Shahid, S., Kabra, A., Pal, R.K., Arora, A.

Revision History  

• Version 1.0: 2017-09-20
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary