2H8G | pdb_00002h8g

5'-Methylthioadenosine Nucleosidase from Arabidopsis thaliana

• PDB DOI: https://doi.org/10.2210/pdb2H8G/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-07 Released: 2006-10-10 
• Deposition Author(s): Park, E.Y., Oh, S.I., Nam, M.J., Shin, J.S., Kim, K.N., Song, H.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Literature

Crystal structure of 5'-methylthioadenosine nucleosidase from Arabidopsis thaliana at 1.5-A resolution

Park, E.Y., Oh, S.I., Nam, M.J., Shin, J.S., Kim, K.N., Song, H.K.

(2006) Proteins 65: 519-523

• PubMed: 16909418 
• DOI: https://doi.org/10.1002/prot.21120
• Primary Citation Related Structures: 
  2H8G

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Organizational Affiliation: 
• School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, 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 (software)

Macromolecule Content 

• Total Structure Weight: 57.22 kDa 
• Atom Count: 4,356 
• Modeled Residue Count: 490 
• Deposited Residue Count: 534 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-Methylthioadenosine Nucleosidase	A, B	267	Arabidopsis thaliana	Mutation(s): 0  Gene Names: AT4g38800 EC: 3.2.2.16
UniProt
Find proteins for Q9T0I8 (Arabidopsis thaliana) Explore Q9T0I8  Go to UniProtKB:  Q9T0I8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADE	C [auth A], D [auth B]	ADENINE C5 H5 N5 GFFGJBXGBJISGV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.543	α = 90
b = 126.585	β = 104.38
c = 45.794	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-10 
Deposition Author(s): Park, E.Y., Oh, S.I., Nam, M.J., Shin, J.S., Kim, K.N., Song, H.K.

Revision History  

• Version 1.0: 2006-10-10
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations