2WQK | pdb_00002wqk

Crystal Structure of Sure Protein from Aquifex aeolicus

• PDB DOI: https://doi.org/10.2210/pdb2WQK/pdb
• Entry: 2WQK supersedes: 2PHJ

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-08-23 Released: 2009-09-29 
• Deposition Author(s): Antonyuk, S.V., Ellis, M.J., Strange, R.W., Hasnain, S.S., Bessho, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structure of Sure Protein from Aquifex Aeolicus Vf5 at 1.5 A Resolution.

Antonyuk, S.V., Ellis, M.J., Strange, R.W., Bessho, Y., Kuramitsu, S., Shinkai, A., Yokoyama, S., Hasnain, S.S.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1204

• PubMed: 20054112 
• DOI: https://doi.org/10.1107/S1744309109043814
• Primary Citation of Related Structures:  
  2WQK


• PubMed Abstract: 
  

  SurE is a stationary-phase survival protein found in bacteria, eukaryotes and archaea that exhibits a divalent-metal-ion-dependent phosphatase activity and acts as a nucleotidase and polyphosphate phosphohydrolase. The structure of the SurE protein from the hyperthermophile Aquifex aeolicus has been solved at 1.5 A resolution using molecular replacement with one dimer in the asymmetric unit and refined to an R factor of 15.6%. The crystal packing reveals that two dimers assemble to form a tetramer, although gel-filtration chromatography showed the presence of only a dimer in solution. The phosphatase active-site pocket was occupied by sulfate ions from the crystallization medium.

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Organizational Affiliation: 

Molecular Biophysics Group, School of Biological Sciences, University of Liverpool, Crown Street, Liverpool L69 7ZB, England.

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 (software)

Macromolecule Content

• Total Structure Weight: 56.63 kDa 
• Atom Count: 4,735 
• Modelled Residue Count: 496 
• Deposited Residue Count: 502 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5'-NUCLEOTIDASE SURE	A, B	251	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: SURE, AQ_832 EC: 3.1.3.5
UniProt
Find proteins for O67004 (Aquifex aeolicus (strain VF5)) Explore O67004  Go to UniProtKB:  O67004

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], E [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	D [auth A], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.006	α = 90
b = 65.006	β = 90
c = 239.194	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Antonyuk, S.V., Ellis, M.J., Strange, R.W., Hasnain, S.S., Bessho, Y., Kuramitsu, S., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)
• This entry supersedes: 2PHJ

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Derived calculations, Other, Source and taxonomy, Version format compliance
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation, Other
• Version 1.3: 2019-08-21
  Changes: Data collection, Database references
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description