1URR

A novel Drosophila Melanogaster Acylphosphatase (AcPDro2)

• PDB DOI: https://doi.org/10.2210/pdb1URR/pdb

• Classification: HYDROLASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-11-03 Released: 2004-05-27 
• Deposition Author(s): Rosano, C., Zuccotti, S., Bolognesi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.230 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 

Starting Model: experimental

Literature

Three-Dimensional Structural Characterization of a Novel Drosophila Melanogaster Acylphosphatase

Zuccotti, S., Rosano, C., Ramazzotti, M., Degl'Innocenti, D., Stefani, M., Manao, G., Bolognesi, M.

(2004) Acta Crystallogr D Biol Crystallogr 60: 1177

• PubMed: 15159593 
• DOI: https://doi.org/10.1107/S0907444904006808
• Primary Citation of Related Structures:  
  1URR


• PubMed Abstract: 
  

  Analysis of the Drosophila melanogaster EST database led to the discovery and cloning of a novel acylphosphatase. The CG18505 gene coding for a new enzyme (AcPDro2) is clearly distinct from the previously described CG16870Acyp gene, which also codes for a D. melanogaster acylphosphatase (AcPDro). The putative catalytic residues, together with residues held to stabilize the acylphosphatase fold, are conserved in the two encoded proteins. Crystals of AcPDro2, which belong to the trigonal space group P3(1)21, with unit-cell parameters a = b = 45.8, c = 98.6 angstroms, gamma = 120 degrees, allowed the solution of the protein structure by molecular replacement and its refinement to 1.5 angstroms resolution. The AcPDro2 active-site structure is discussed.

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Organizational Affiliation: 

Department of Physics-INFM and Center of Excellence for Biomedical Research, University of Genova, Via Dodecaneso 33, 16132 Genova, Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 11.88 kDa 
• Atom Count: 918 
• Modelled Residue Count: 97 
• Deposited Residue Count: 102 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CG18505 PROTEIN	A	102	Drosophila melanogaster	Mutation(s): 0  EC: 3.6.1.7
UniProt
Find proteins for Q9VF36 (Drosophila melanogaster) Explore Q9VF36  Go to UniProtKB:  Q9VF36

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	B [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.230 
• R-Value Work: 0.160 
• R-Value Observed: 0.163 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.722	α = 90
b = 45.722	β = 90
c = 98.585	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-05-27 
Deposition Author(s): Rosano, C., Zuccotti, S., Bolognesi, M.

Revision History  

• Version 1.0: 2004-05-27
  Type: Initial release
  
• Version 1.1: 2014-02-19
  Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description