3KK0 | pdb_00003kk0

Crystal structure of partially folded intermediate state of peptidyl-tRNA hydrolase from Mycobacterium smegmatis

• PDB DOI: https://doi.org/10.2210/pdb3KK0/pdb

• Classification: HYDROLASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-11-04 Released: 2010-11-10 
• Deposition Author(s): Kumar, A., Singh, N., Yadav, R., Sharma, S., Arora, A., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structures of Fully-Folded Native and Partially-Folded Intermediate States of Peptidyl-tRNA Hydrolase from Mycobacterium smegmatis

Kumar, A., Singh, N., Yadav, R., 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)

Macromolecule Content

• Total Structure Weight: 20.88 kDa 
• Atom Count: 1,636 
• Modelled Residue Count: 191 
• Deposited Residue Count: 191 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-tRNA hydrolase	A	191	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  EC: 3.1.1.29
UniProt
Find proteins for A0R3D3 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R3D3  Go to UniProtKB:  A0R3D3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	I [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
BME	J [auth A]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO	E [auth A], F [auth A], G [auth A], H [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
IPA	B [auth A], C [auth A], D [auth A]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.241 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.223 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.006	α = 90
b = 65.597	β = 90
c = 68.69	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-11-10 
Deposition Author(s): Kumar, A., Singh, N., Yadav, R., Sharma, S., Arora, A., Singh, T.P.

Revision History  

• Version 1.0: 2010-11-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description