1QHW

PURPLE ACID PHOSPHATASE FROM RAT BONE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Three-dimensional structure of a mammalian purple acid phosphatase at 2.2 A resolution with a mu-(hydr)oxo bridged di-iron center.

Lindqvist, Y.Johansson, E.Kaija, H.Vihko, P.Schneider, G.

(1999) J Mol Biol 291: 135-147

  • DOI: 10.1006/jmbi.1999.2962
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The crystal structure of purple acid phosphatase from rat bone has been determined by molecular replacement and the structure has been refined to 2.2 A resolution to an R -factor of 21.3 % (R -free 26.5 %). The core of the enzyme consists of two seve ...

    The crystal structure of purple acid phosphatase from rat bone has been determined by molecular replacement and the structure has been refined to 2.2 A resolution to an R -factor of 21.3 % (R -free 26.5 %). The core of the enzyme consists of two seven-stranded mixed beta-sheets, with each sheet flanked by solvent-exposed alpha-helices on one side. The two sheets pack towards each other forming a beta-sandwich. The di-iron center, located at the bottom of the active-site pocket at one edge of the beta-sandwich, contains a mu-hydroxo or mu-oxo bridge and both metal ions are observed in an almost perfect octahedral coordination geometry. The electron density map indicates that a mu-(hydr)oxo bridge is found in the metal center and that at least one solvent molecule is located in the first coordination sphere of one of the metal ions. The crystallographic study of rat purple acid phosphatase reveals that the mammalian enzymes are very similar in overall structure to the plant enzymes in spite of only 18 % overall sequence identity. In particular, coordination and geometry of the iron cluster is preserved in both enzymes and comparison of the active-sites suggests a common mechanism for the mammalian and plant enzymes. However, significant differences are found in the architecture of the substrate binding pocket.


    Related Citations: 
    • Tartrate-Resistant Bone Acid Phosphatase: Large-Scale Production and Purification of the Recombinant Enzyme, Characterization, and Crystallization
      Kaija, H., Jia, J., Lindqvist, Y., Andersson, G., Vihko, P.
      (1999) J Bone Miner Res 14: 424

    Organizational Affiliation

    Department of Medical Biochemistry & Biophysics, Karolinska Institutet, Stockholm, S-171 77, Sweden. ylva@alfa.mbb.ki.se



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PURPLE ACID PHOSPHATASE)
A
327Rattus norvegicusMutation(s): 0 
Gene Names: Acp5
EC: 3.1.3.2
Find proteins for P29288 (Rattus norvegicus)
Go to UniProtKB:  P29288
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.98α = 90
b = 88.12β = 90
c = 57.07γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-09-15
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance