1B8J | pdb_00001b8j

ALKALINE PHOSPHATASE COMPLEXED WITH VANADATE

PDB DOI: https://doi.org/10.2210/pdb1B8J/pdb

Classification: ALKALINE PHOSPHATASE
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 1999-02-01 Released: 1999-02-18
Deposition Author(s): Holtz, K.M., Stec, B., Kantrowitz, E.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.196 (Depositor)
R-Value Work:
0.177 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Literature

A model of the transition state in the alkaline phosphatase reaction.

Holtz, K.M., Stec, B., Kantrowitz, E.R.

(1999) J Biol Chem 274: 8351-8354

PubMed: 10085061 Search on PubMed
DOI: https://doi.org/10.1074/jbc.274.13.8351
Primary Citation Related Structures:
1B8J

PubMed Abstract:
A high resolution crystal structure of Escherichia coli alkaline phosphatase in the presence of vanadate has been refined to 1.9 A resolution. The vanadate ion takes on a trigonal bipyramidal geometry and is covalently bound by the active site serine nucleophile. A coordinated water molecule occupies the axial position opposite the serine nucleophile, whereas the equatorial oxygen atoms of the vanadate ion are stabilized by interactions with both Arg-166 and the zinc metal ions of the active site. This structural complex supports the in-line displacement mechanism of phosphomonoester hydrolysis by alkaline phosphatase and provides a model for the proposed transition state in the enzyme-catalyzed reaction.

Organizational Affiliation

Department of Chemistry, Merkert Chemistry Center, Boston College, Chestnut Hill, Massachusetts 02167, USA.

Macromolecule Content

Total Structure Weight: 94.92 kDa
Atom Count: 7,579
Modeled Residue Count: 898
Deposited Residue Count: 898
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ALKALINE PHOSPHATASE)	A, B	449	Escherichia coli	Mutation(s): 0 Gene Names: PHOA EC: 3.1.3.1
UniProt
Find proteins for P00634 (Escherichia coli (strain K12)) Explore P00634 Go to UniProtKB: P00634
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00634
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VO4 Query on VO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	VANADATE ION O₄ V LSGOVYNHVSXFFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain J [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B]	C [auth A], D [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain H [auth B] Focus chain I [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain F [auth A]	F [auth A], K [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.196 (Depositor)
R-Value Work: 0.177 (Depositor)

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 195.41	α = 90
b = 167.81	β = 90
c = 76.52	γ = 90

Software Package:

Software Name	Purpose
SDMS	data collection
SDMS	data reduction
X-PLOR	model building
X-PLOR	refinement
SDMS	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1999-02-18

Deposition Author(s):

Holtz, K.M.

Stec, B.

Kantrowitz, E.R.

Revision History (Full details and data files)

Version 1.0: 1999-02-18
Type: Initial release
Version 1.1: 2007-10-16
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-04
Changes: Refinement description
Version 1.4: 2023-08-09
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-10-16
Changes: Structure summary
Version 2.0: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Polymer sequence, Structure summary