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- PDB-1es9: X-RAY CRYSTAL STRUCTURE OF R22K MUTANT OF THE MAMMALIAN BRAIN PLA... -

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Basic information

Entry
Database: PDB / ID: 1es9
TitleX-RAY CRYSTAL STRUCTURE OF R22K MUTANT OF THE MAMMALIAN BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASES (PAF-AH)
ComponentsPLATELET-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 / 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
Platelet-activating factor acetylhydrolase IB subunit alpha1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.3 Å
AuthorsMcMullen, T.W.P. / Li, J. / Sheffield, P.J. / Aoki, J. / Martin, T.W. / Arai, H. / Inoue, K. / Derewenda, Z.S.
Citation
Journal: Protein Eng. / Year: 2000
Title: The functional implications of the dimerization of the catalytic subunits of the mammalian brain platelet-activating factor acetylhydrolase (Ib).
Authors: McMullen, T.W. / Li, J. / Sheffield, P.J. / Aoki, J. / Martin, T.W. / Arai, H. / Inoue, K. / 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
DepositionApr 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation
Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _exptl_crystal_grow.temp
Revision 1.4Nov 3, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB GAMMA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)25,8751
Polymers25,8751
Non-polymers00
Water5,350297
1
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB GAMMA SUBUNIT

A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE IB GAMMA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)51,7512
Polymers51,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Unit cell
Length a, b, c (Å)81.049, 81.049, 72.662
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a dimer

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Components

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


Mass: 25875.350 Da / Num. of mol.: 1 / Mutation: R22K / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: BRAIN
References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.66 Å3/Da / Density % sol: 53.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.6M Ammonium sulphate, 100mM sodium acetate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop / Details: Ho, Y.S., (1999) Protein Eng., 12, 693.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-9 mg/mlprotein1drop
212-18 %ammonium sulfate1reservoir
3Tris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9724
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 14, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. all: 85358 / Num. obs: 72050 / % possible obs: 84.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.4 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 32
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2 % / Rmerge(I) obs: 0.448 / Num. unique all: 7738 / % possible all: 87.4
Reflection
*PLUS
Num. obs: 85358 / % possible obs: 98.7 % / Num. measured all: 461423
Reflection shell
*PLUS
% possible obs: 90.4 % / Rmerge(I) obs: 0.366

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.3→10 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2684 -random
Rwork0.192 ---
all0.192 67828 --
obs0.192 67828 14.7 %-
Refinement stepCycle: LAST / Resolution: 1.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 0 340 2027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.023
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Type: p_planar_d / Dev ideal: 0.024

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