6LSP | pdb_00006lsp

Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.50 A resolution reveals an inhibited form.

• PDB DOI: https://doi.org/10.2210/pdb6LSP/pdb

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


• Deposited: 2020-01-18 Released: 2020-02-05 
• Deposition Author(s): Viswanathan, V., Ahmad, M.I., Sharma, P., Sharma, S., Singh, T.P.
• Funding Organization(s): Department of Science & Technology (DST, India)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a dimeric Piptidyl t-RNA hydrolase from Acinetobacter baumannii at 1.50 A resolution reveals on inhibited form.

Viswanathan, V., Ahmad, M.I., Sharma, P., Sharma, S., Singh, T.P.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 41.94 kDa 
• Atom Count: 3,624 
• Modeled Residue Count: 386 
• Deposited Residue Count: 386 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A, B	193	Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841	Mutation(s): 0  Gene Names: pth, BIT33_16330, 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.197 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.58	α = 90
b = 98.54	β = 90
c = 123.67	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Viswanathan, V., Ahmad, M.I., Sharma, P., Sharma, S., Singh, T.P.

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Funding Organization	Location	Grant Number
Department of Science & Technology (DST, India)	India	PDF/2018/000008

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description