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- PDB-1fxw: CRYSTAL STRUCTURE OF THE RECOMBINANT ALPHA1/ALPHA2 CATALYTIC HETE... -

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Basic information

Entry
Database: PDB / ID: 1fxw
TitleCRYSTAL STRUCTURE OF THE RECOMBINANT ALPHA1/ALPHA2 CATALYTIC HETERODIMER OF BOVINE BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB.
Components
  • PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
  • PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB GAMMA SUBUNIT
KeywordsHYDROLASE / alpha beta hydrolase fold
Function / homology
Function and homology information


platelet-activating factor acetyltransferase activity / 1-alkyl-2-acetylglycerophosphocholine esterase complex / 1-alkyl-2-acetylglycerophosphocholine esterase / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Neutrophil degranulation / positive regulation of macroautophagy / lipid catabolic process / fibrillar center / spermatogenesis ...platelet-activating factor acetyltransferase activity / 1-alkyl-2-acetylglycerophosphocholine esterase complex / 1-alkyl-2-acetylglycerophosphocholine esterase / COPI-independent Golgi-to-ER retrograde traffic / 1-alkyl-2-acetylglycerophosphocholine esterase activity / Neutrophil degranulation / positive regulation of macroautophagy / lipid catabolic process / fibrillar center / spermatogenesis / protein heterodimerization activity / protein homodimerization activity / plasma membrane / cytoplasm / cytosol
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
Platelet-activating factor acetylhydrolase IB subunit alpha2 / Platelet-activating factor acetylhydrolase IB subunit alpha1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsDerewenda, Z. / Li, J.
Citation
Journal: Protein Eng. / Year: 2001
Title: Preparation and crystal structure of the recombinant alpha(1)/alpha(2) catalytic heterodimer of bovine brain platelet-activating factor acetylhydrolase Ib.
Authors: Sheffield, P.J. / McMullen, T.W. / Li, J. / Ho, Y.S. / Garrard, S.M. / Derewenda, U. / Derewenda, Z.S.
#1: 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.
History
DepositionSep 27, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 IB GAMMA SUBUNIT
F: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5443
Polymers51,5042
Non-polymers401
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-17 kcal/mol
Surface area17430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.519, 80.848, 116.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is alpha1/alpha1 homodimer, alpha1/alpha2 heterodimer and alpha2/alpha2 homodimer

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Components

#1: Protein PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB GAMMA SUBUNIT / ALPHA1


Mass: 25903.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: BRAIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Protein PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB BETA SUBUNIT / ALPHA2


Mass: 25600.264 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Organ: BRAIN / Production host: Escherichia coli (E. coli)
References: UniProt: P68401, 1-alkyl-2-acetylglycerophosphocholine esterase
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / 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: 2.03 Å3/Da / Density % sol: 39.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 17% PEG-MME 2000, 100 mM Na acetate, pH 6.4, 10 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
117 %PEG2000 MME11
2100 mMsodium acetate11
310 mM11CaCl2
412 mg/mlprotein11

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0084
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Jul 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0084 Å / Relative weight: 1
ReflectionResolution: 2.07→20 Å / Num. all: 26093 / Num. obs: 25752 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.83 % / Biso Wilson estimate: 30.98 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.63
Reflection shellResolution: 2.07→20 Å / Redundancy: 3.47 % / Rmerge(I) obs: 0.371 / Num. unique all: 2848 / % possible all: 99.1
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. obs: 25073 / % possible obs: 99.1 % / Num. measured all: 273571 / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.18 Å / % possible obs: 99.4 % / Rmerge(I) obs: 0.335

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / σ(F): 1 / σ(I): 1 / Stereochemistry target values: Engh & Huber
Details: residues A53 to A63 were not included in the final refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.275 220 -random
Rwork0.218 ---
all0.21 25202 --
obs0.212 22999 99.1 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3348 0 1 121 3470
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.23
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / σ(F): 1 / Rfactor obs: 0.218 / Rfactor Rfree: 0.277
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.009
X-RAY DIFFRACTIONp_angle_d0.023
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.027
X-RAY DIFFRACTIONp_plane_restr9.1

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