1V4N | pdb_00001v4n

Structure of 5'-deoxy-5'-methylthioadenosine phosphorylase homologue from Sulfolobus tokodaii

• PDB DOI: https://doi.org/10.2210/pdb1V4N/pdb

• Classification: TRANSFERASE
• Organism(s): Sulfurisphaera tokodaii
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-14 Released: 2005-01-04 
• Deposition Author(s): Kitago, Y., Yasutake, Y., Sakai, N., Tsujimura, M., Yao, M., Watanabe, N., Kawarabayasi, Y., Tanaka, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.191 (DCC) 

Starting Model: experimental

Literature

Crystal structure of Sulfolobus tokodaii MTAP

Kitago, Y., Yasutake, Y., Sakai, N., Tsujimura, M., Yao, M., Watanabe, N., Kawarabayasi, Y., Tanaka, I.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Macromolecule Content 

• Total Structure Weight: 94.75 kDa 
• Atom Count: 6,539 
• Modeled Residue Count: 802 
• Deposited Residue Count: 843 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
271aa long hypothetical 5'-methylthioadenosine phosphorylase	A, B, C	281	Sulfurisphaera tokodaii	Mutation(s): 0  Gene Names: ST0485 EC: 2.4.2.28
UniProt
Find proteins for F9VN03 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore F9VN03  Go to UniProtKB:  F9VN03

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.241 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.191 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.869	α = 90
b = 142.888	β = 90
c = 169.564	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-04 
Deposition Author(s): Kitago, Y., Yasutake, Y., Sakai, N., Tsujimura, M., Yao, M., Watanabe, N., Kawarabayasi, Y., Tanaka, I.

Revision History  

• Version 1.0: 2005-01-04
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary