2NX8

The crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

• PDB DOI: https://doi.org/10.2210/pdb2NX8/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pyogenes serotype M6
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-11-17 Released: 2007-08-21 
• Deposition Author(s): Hwang, K.Y., Lee, W.-H., Kim, Y.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

Crystal structure of the tRNA-specific adenosine deaminase from Streptococcus pyogenes

Lee, W.-H., Kim, Y.K., Nam, K.H., Priyadarshi, A., Lee, E.H., Kim, E.E., Jeon, Y.H., Cheong, C., Hwang, K.Y.

(2007) Proteins 68: 1016-1019

• PubMed: 17554781 
• DOI: https://doi.org/10.1002/prot.21456
• Primary Citation of Related Structures:  
  2NX8

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Organizational Affiliation: 

Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Seoul 136-701, South Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 20.4 kDa 
• Atom Count: 1,470 
• Modelled Residue Count: 168 
• Deposited Residue Count: 179 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRNA-specific adenosine deaminase	A	179	Streptococcus pyogenes serotype M6	Mutation(s): 2  EC: 3.5.4 (PDB Primary Data), 3.5.4.33 (UniProt)
UniProt
Find proteins for Q5XE14 (Streptococcus pyogenes serotype M6 (strain ATCC BAA-946 / MGAS10394)) Explore Q5XE14  Go to UniProtKB:  Q5XE14

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.242 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.091	α = 90
b = 80.091	β = 90
c = 81.104	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-08-21 
Deposition Author(s): Hwang, K.Y., Lee, W.-H., Kim, Y.K.

Revision History  

• Version 1.0: 2007-08-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2021-11-10
  Changes: Database references, Derived calculations
• Version 1.3: 2023-12-27
  Changes: Data collection