6KL8 | pdb_00006kl8

Crystal structure of Piptidyl t-RNA hydrolase from Acinetobacter baumannii with bound NaCl at the substrate binding site

• PDB DOI: https://doi.org/10.2210/pdb6KL8/pdb

• Classification: HYDROLASE
• Organism(s): Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-07-29 Released: 2019-08-07 
• Deposition Author(s): Viswanathan, V., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 
  0.164 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.141 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Piptidyl t-RNA hydrolase from Acinetobacter baumannii with bound NaCl at the substrate binding site

Viswanathan, V., Sharma, P., Singh, P.K., Sharma, S., 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)

Macromolecule Content 

• Total Structure Weight: 21.37 kDa 
• Atom Count: 1,691 
• Modeled Residue Count: 196 
• Deposited Residue Count: 196 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	196	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0  Gene Names: pth, HMPREF0010_01329 EC: 3.1.1.29
UniProt
Find proteins for D0C9L6 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81)) Explore D0C9L6  Go to UniProtKB:  D0C9L6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO (Subject of Investigation/LOI)	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free:  0.164 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.141 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.961	α = 90
b = 66.099	β = 90
c = 75.825	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Viswanathan, V., Sharma, P., Singh, P.K., Sharma, S., Singh, T.P.

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description