Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 86.81 kDa 
• Atom Count: 6862 
• Residue Count: 798 
• Unique protein chains: 1

3A52

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

• DOI: 10.2210/pdb3A52/pdb

• Classification: HYDROLASE
• Organism(s): Shewanella sp. AP1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-24 Released: 2010-04-14 
• Deposition Author(s): Tsuruta, H., Mikami, B., Higashi, T., Aizono, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 

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

• PubMed: 20057143 
• DOI: 10.1271/bbb.90563
• Primary Citation of Related Structures:  
  3A52


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cold-active alkaline phosphatase	A, B	400	Shewanella sp. AP1	Mutation(s): 0  Gene Names: scap
Find proteins for Q8RQU7 (Shewanella sp. AP1) Explore Q8RQU7  Go to UniProtKB:  Q8RQU7

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	A, B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.244 
• R-Value Work: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.059	α = 90
b = 95.863	β = 101.62
c = 71.058	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-07-24 
• Released Date: 2010-04-14 
Deposition Author(s): Tsuruta, H., Mikami, B., Higashi, T., Aizono, Y.

Revision History 

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