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): Yes 


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

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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

Literature

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

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

(1999) J Biological Chem 274: 8351-8354

• PubMed: 10085061 
• DOI: https://doi.org/10.1074/jbc.274.13.8351
• Primary Citation of 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

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

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

Macromolecule Content

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (ALKALINE PHOSPHATASE)	A, B	449	Escherichia coli	Mutation(s): 1  Gene Names: PHOA EC: 3.1.3.1
UniProt
Find proteins for P00634 (Escherichia coli (strain K12)) Explore P00634  Go to UniProtKB:  P00634

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A], I [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	C [auth A], D [auth A], G [auth B], H [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	F [auth A], J [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SVA	A, B	L-PEPTIDE LINKING	C3 H7 N O7 V		SER

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

Entry History 

Deposition Data

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

Revision History  

• 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