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- PDB-1wab: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE -

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Basic information

Entry
Database: PDB / ID: 1wab
TitlePLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
ComponentsPLATELET-ACTIVATING FACTOR ACETYLHYDROLASE1-alkyl-2-acetylglycerophosphocholine esterase
KeywordsPLATELET FACTOR / OXIDOREDUCTASE / FLAVOPROTEIN / FAD / PEROXISOME
Function / homology
Function and homology information


platelet-activating factor acetyltransferase activity / 1-alkyl-2-acetylglycerophosphocholine esterase complex / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid catabolic process / spermatogenesis / protein heterodimerization activity / protein homodimerization activity / cytoplasm
Similarity search - Function
SGNH hydrolase / SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Platelet-activating factor acetylhydrolase IB subunit alpha1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsHo, Y.S. / Swenson, L. / Derewenda, U. / Serre, L. / Wei, Y. / Dauter, Z. / Hattori, M. / Aoki, J. / Arai, H. / Adachi, T. ...Ho, Y.S. / Swenson, L. / Derewenda, U. / Serre, L. / Wei, Y. / Dauter, Z. / Hattori, M. / Aoki, J. / Arai, H. / Adachi, T. / Inoue, K. / Derewenda, Z.S.
Citation
Journal: Nature / Year: 1997
Title: Brain acetylhydrolase that inactivates platelet-activating factor is a G-protein-like trimer.
Authors: Ho, Y.S. / Swenson, L. / Derewenda, U. / Serre, L. / Wei, Y. / Dauter, Z. / Hattori, M. / Adachi, T. / Aoki, J. / Arai, H. / Inoue, K. / Derewenda, Z.S.
#1: Journal: J.Biol.Chem. / Year: 1994
Title: The Catalytic Subunit of Bovine Brain Platelet-Activating Factor Acetylhydrolase is a Novel Type of Serine Esterase
Authors: Hattori, M. / Adachi, H. / Tsujimoto, M. / Arai, H. / Inoue, K.
History
DepositionOct 30, 1996Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9622
Polymers25,9031
Non-polymers591
Water4,179232
1
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
hetero molecules

A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9254
Polymers51,8072
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)81.260, 81.260, 72.600
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-528-

HOH

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Components

#1: Protein PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / 1-alkyl-2-acetylglycerophosphocholine esterase / PAF-AH


Mass: 25903.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: WITH ACETATE BOUND / Source: (natural) Bos taurus (cattle) / Organ: BRAIN
References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 48.5 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.15-3.15 mg/mlprotein1drop
25 mMTris-HCl1drop
31 mMDTT1drop
48 %satammonium sulfate1drop
5100 mMsodium acetate1drop
616 %satammonium sulfate1reservoir
7200 mMsodium acetate1reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.859
DetectorType: MARRESEARCH / Date: Nov 25, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.859 Å / Relative weight: 1
ReflectionNum. obs: 33716 / % possible obs: 99.7 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.063
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 20 Å / Num. measured all: 387544

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
REFMACrefinement
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 1.7→8.5 Å /
RfactorNum. reflection
Rwork0.1954 -
obs-30578
Displacement parametersBiso mean: 23.1 Å2
Refinement stepCycle: LAST / Resolution: 1.7→8.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 4 232 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.2
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1083
X-RAY DIFFRACTIONp_mcangle_it2.855
X-RAY DIFFRACTIONp_scbond_it4.3726
X-RAY DIFFRACTIONp_scangle_it5.9738
X-RAY DIFFRACTIONp_plane_restr0.050.04
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2560.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1710.3
X-RAY DIFFRACTIONp_planar_tor5.73
X-RAY DIFFRACTIONp_staggered_tor16.78
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor36.310
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.1954
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.108 Å2
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.034

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