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- PDB-1bwp: PROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLAT... -

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Basic information

Entry
Database: PDB / ID: 1bwp
TitlePROBING THE SUBSTRATE SPECIFICITY OF THE INTRACELLULAR BRAIN PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
ComponentsPLATELET-ACTIVATING FACTOR ACETYLHYDROLASE
KeywordsHYDROLASE / ACETYLHYDROLASE HYDROLASE / LIPID DEGRADATION / PLATELET FACTOR
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-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase / 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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHo, Y.S. / Sheffield, P.J. / Masuyama, J. / Arai, H. / Li, J. / Aoki, J. / Inoue, K. / Derewenda, U. / Derewenda, Z.
Citation
Journal: Protein Eng. / Year: 1999
Title: Probing the Substrate Specificity of the Intracellular Brain Platelet-Activating Factor Acetylhydrolase
Authors: Ho, Y.S. / Sheffield, P.J. / Masuyama, J. / Arai, H. / Li, J. / Aoki, J. / Inoue, K. / 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, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE


Theoretical massNumber of molelcules
Total (without water)25,9581
Polymers25,9581
Non-polymers00
Water2,612145
1
A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE

A: PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE


Theoretical massNumber of molelcules
Total (without water)51,9172
Polymers51,9172
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)81.800, 81.800, 72.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / PAFAH


Mass: 25958.400 Da / Num. of mol.: 1 / Mutation: L48A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Tissue: BRAIN / Cellular location: CYTOPLASM / Organ: BRAIN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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 Å3/Da / Density % sol: 39 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-9 mg/mlprotein1drop
216 %ammonium sulfate1reservoir
3Tris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 16524 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 10.56 % / Rsym value: 0.046 / Net I/σ(I): 16.2
Reflection shellResolution: 2.1→2.17 Å / Rsym value: 0.199 / % possible all: 71
Reflection
*PLUS
Num. measured all: 174619 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 70.8 % / Rmerge(I) obs: 0.203

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PAF ACETYLHYDROLASE

Resolution: 2.1→8 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1635 10 %RANDOM
Rwork0.209 ---
obs-16355 99 %-
Displacement parametersBiso mean: 22.56 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1687 0 0 145 1832
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.025
X-RAY DIFFRACTIONp_angle_d0.0230.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr9.410
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2440.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS

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