2ZAU | pdb_00002zau

Crystal structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2ZAU/pdb

• Classification: TRANSFERASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-10-10 Released: 2008-06-17 
• Deposition Author(s): Sekine, S., Matsumoto, E., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Literature

Structure of an N-terminally truncated selenophosphate synthetase from Aquifex aeolicus

Matsumoto, E., Sekine, S., Akasaka, R., Otta, Y., Katsura, K., Inoue, M., Kaminishi, T., Terada, T., Shirouzu, M., Yokoyama, S.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 453-458

• PubMed: 18540050 
• DOI: https://doi.org/10.1107/S1744309108012074
• Primary Citation Related Structures: 
  2ZAU


• PubMed Abstract: 
  

  Selenophosphate synthetase (SPS) catalyzes the activation of selenide with ATP to synthesize selenophosphate, the reactive selenium donor for biosyntheses of both the 21st amino acid selenocysteine and 2-selenouridine nucleotides in tRNA anticodons. The crystal structure of an N-terminally (25 residues) truncated fragment of SPS (SPS-DeltaN) from Aquifex aeolicus has been determined at 2.0 A resolution. The structure revealed SPS to be a two-domain alpha/beta protein, with domain folds that are homologous to those of PurM-superfamily proteins. In the crystal, six monomers of SPS-DeltaN form a hexamer of 204 kDa, whereas the molecular weight estimated by ultracentrifugation was approximately 63 kDa, which is comparable to the calculated weight of the dimer (68 kDa).

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Organizational Affiliation: 
• Systems and Structural Biology Center, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.

Biological Assembly 1  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

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

Macromolecule Content 

• Total Structure Weight: 103.08 kDa 
• Atom Count: 7,533 
• Modeled Residue Count: 914 
• Deposited Residue Count: 933 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Selenide, water dikinase	A, B, C	311	Aquifex aeolicus	Mutation(s): 0  Gene Names: selD EC: 2.7.9.3
UniProt
Find proteins for O67139 (Aquifex aeolicus (strain VF5)) Explore O67139  Go to UniProtKB:  O67139

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	D [auth A], E [auth B], F [auth C]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.161	α = 90
b = 165.198	β = 90
c = 167.684	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-17 
Deposition Author(s): Sekine, S., Matsumoto, E., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-06-17
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-10-30
  Changes: Data collection, Database references, Derived calculations, Structure summary