4DHW | pdb_00004dhw

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with Adipic acid at 2.4 Angstrom resolution

• PDB DOI: https://doi.org/10.2210/pdb4DHW/pdb

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-01-30 Released: 2012-02-29 
• Deposition Author(s): Kumar, A., Singh, A., Singh, N., Sinha, M., Sharma, S., Arora, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.206 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.192 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Peptidyl-tRNA hydrolase from Pseudomonas aeruginosa with Adipic acid at 2.4 Angstrom resolution

Kumar, A., Singh, A., Singh, N., Sinha, M., Sharma, S., Arora, A., Singh, T.P.

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 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: 41.96 kDa 
• Atom Count: 3,142 
• Modeled Residue Count: 388 
• Deposited Residue Count: 388 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	194	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA4672, pth EC: 3.1.1.29
UniProt
Find proteins for Q9HVC3 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HVC3  Go to UniProtKB:  Q9HVC3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0L1	C [auth A], D [auth B]	hexanedioic acid C6 H10 O4 WNLRTRBMVRJNCN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.206 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.192 (DCC) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.594	α = 90
b = 64.594	β = 90
c = 156.245	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-29 
Deposition Author(s): Kumar, A., Singh, A., Singh, N., Sinha, M., Sharma, S., Arora, A., Singh, T.P.

Revision History  

• Version 1.0: 2012-02-29
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description