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- PDB-1urr: A novel Drosophila Melanogaster Acylphosphatase (AcPDro2) -

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Basic information

Entry
Database: PDB / ID: 1urr
TitleA novel Drosophila Melanogaster Acylphosphatase (AcPDro2)
ComponentsCG18505 PROTEIN
KeywordsHYDROLASE / ACYLPHOSPHATASE / ENZYME
Function / homology
Function and homology information


cellular metabolic process / acylphosphatase / acylphosphatase activity / hydrolase activity / cytoplasm
Similarity search - Function
Acylphosphatase / Acylphosphatase signature 1. / Acylphosphatase, conserved site / Acylphosphatase / Acylphosphatase-like domain / Acylphosphatase-like domain profile. / Acylphosphatase-like domain superfamily / Alpha-Beta Plaits - #100 / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRosano, C. / Zuccotti, S. / Bolognesi, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Three-Dimensional Structural Characterization of a Novel Drosophila Melanogaster Acylphosphatase
Authors: Zuccotti, S. / Rosano, C. / Ramazzotti, M. / Degl'Innocenti, D. / Stefani, M. / Manao, G. / Bolognesi, M.
#1: Journal: FEBS Lett. / Year: 2003
Title: Characterization of a Novel Drosophila Melanogaster Acylphosphatase
Authors: Degl'Innocenti, D. / Ramazzotti, M. / Marzocchini, R. / Chiti, F. / Raugei, G.
History
DepositionNov 3, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CG18505 PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,8762
Polymers11,7841
Non-polymers921
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.722, 45.722, 98.585
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-2051-

HOH

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Components

#1: Protein CG18505 PROTEIN / ACYLPHOSPHATASE / ACYLPHPHTASE / ACYP2 / CG18505


Mass: 11783.540 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9VF36, acylphosphatase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 55.2 %
Crystal growpH: 4.5 / Details: pH 4.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.5→39.5 Å / Num. obs: 19859 / % possible obs: 98.7 % / Observed criterion σ(I): 3 / Redundancy: 6.2 % / Biso Wilson estimate: 29.5 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.2
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / % possible all: 97.1

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ACY

2acy


Resolution: 1.5→10 Å / SU ML: 0.047 / ESU R Free: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.23 999 5 %RANDOM
Rwork0.16 ---
obs0.163 18931 98.4 %-
Displacement parametersBiso mean: 26.9 Å2
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 6 109 913

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