3A52

Crystal structure of cold-active alkailne phosphatase from psychrophile Shewanella sp.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of cold-active alkaline phosphatase from the psychrophile Shewanella sp.

Tsuruta, H.Mikami, B.Higashi, T.Aizono, Y.

(2010) Biosci.Biotechnol.Biochem. 74: 69-74

  • DOI: 10.1271/bbb.90563

  • PubMed Abstract: 
  • The crystal structure of a cold-active alkaline phosphatase from a psychrophile, Shewanella sp. (SCAP), was solved at 2.2 A. A refined model showed a homodimer with six metal-ligand sites. The arrangement of the catalytic residues resembled those of ...

    The crystal structure of a cold-active alkaline phosphatase from a psychrophile, Shewanella sp. (SCAP), was solved at 2.2 A. A refined model showed a homodimer with six metal-ligand sites. The arrangement of the catalytic residues resembled those of alkaline phosphatases (APs), suggesting that the reaction mechanism of SCAP was fundamentally identical to those of other APs. SCAP had two distinct structural features: (i) a loop with Arg122 that bound to the phosphate moiety of the substrate suffered no constraints from the linkage to other secondary structures, and (ii) Mg3-ligand His109 was considered to undergo repulsive effect with neighboring Trp228. The local flexibility led by these features might be an important factor in the high catalytic efficiency of SCAP at low temperatures.


    Organizational Affiliation

    Office of Collaborative Research and Technology Development, Kobe University, Hyogo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cold-active alkaline phosphatase
A, B
400Shewanella sp. AP1Mutation(s): 0 
Gene Names: scap
Find proteins for Q8RQU7 (Shewanella sp. AP1)
Go to UniProtKB:  Q8RQU7
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.059α = 90.00
b = 95.863β = 101.62
c = 71.058γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-11
    Type: Refinement description
  • Version 1.3: 2019-10-09
    Type: Data collection, Database references