2EF7 | pdb_00002ef7

Crystal structure of ST2348, a hypothetical protein with CBS domains from Sulfolobus tokodaii strain7

• PDB DOI: https://doi.org/10.2210/pdb2EF7/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-21 Released: 2007-08-21 
• Deposition Author(s): Agari, Y., Karthe, P., Kumarevel, T., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.260 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Literature

Crystal structure of ST2348, a CBS domain protein, from hyperthermophilic archaeon Sulfolobus tokodaii

Ragunathan, P., Kumarevel, T., Agari, Y., Shinkai, A., Kuramitsu, S., Yokoyama, S., Ponnuraj, K.

(2008) Biochem Biophys Res Commun 375: 124-128

• PubMed: 18691556 
• DOI: https://doi.org/10.1016/j.bbrc.2008.07.140
• Primary Citation Related Structures: 
  2EF7


• PubMed Abstract: 
  

  The crystal structure of a hypothetical protein ST2348 (GI: 47118305) from the hyperthermophilic bacteria Sulfolobus tokodaii has been determined using X-ray crystallography. The protein consists of two CBS (cystathione beta synthase) domains, whose function has been analyzed and reported here. PSI-BLAST shows a conservation of this domain in about 100 proteins in various species. However, none of the close homologs of ST2348 have been functionally characterized so far. Structure and sequence comparison of ST2348 with human AMP-kinase gamma1 subunit and the CBS domain pair of bacterial IMP dehydrogenase is suggestive of its binding to AMP and ATP. A highly conserved residue Asp118, located in a negatively charged patch near the ligand binding cleft, could serve as a site for phosphorylation similar to that found in the chemotatic signal protein CheY and thereby ST2348 can function as a signal transduction molecule.

---

Organizational Affiliation: 
• Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 30.29 kDa 
• Atom Count: 2,084 
• Modeled Residue Count: 253 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ST2348	A, B	133	Sulfurisphaera tokodaii str. 7	Mutation(s): 0
UniProt
Find proteins for Q96Y20 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96Y20  Go to UniProtKB:  Q96Y20

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.260 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.221 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.42	α = 90
b = 135.272	β = 90
c = 41.234	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
BSS	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): Agari, Y., Karthe, P., Kumarevel, T., Yokoyama, S., Kuramitsu, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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: 2024-11-13
  Changes: Data collection, Database references, Derived calculations, Structure summary