3A52 | pdb_00003a52

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

PDB DOI: https://doi.org/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.244 (Depositor), 0.244 (DCC)
R-Value Work:
0.183 (Depositor), 0.183 (DCC)

wwPDB Validation 3D Report Full Report

This is version 1.4 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

PubMed: 20057143 Search on PubMed
DOI: https://doi.org/10.1271/bbb.90563
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 86.81 kDa
Atom Count: 6,862
Modeled Residue Count: 798
Deposited Residue Count: 800
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
UniProt
Find proteins for Q8RQU7 (Shewanella sp. AP1) Explore Q8RQU7 Go to UniProtKB: Q8RQU7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8RQU7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B]	C [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B] Focus chain H [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	E [auth A], F [auth A], J [auth B], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.244 (Depositor), 0.244 (DCC)
R-Value Work: 0.183 (Depositor), 0.183 (DCC)

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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-04-14

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.4: 2024-03-13
Changes: Data collection, Database references, Derived calculations