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- PDB-3f97: Crystal structure of human plasma platelet activating factor acet... -

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Basic information

Entry
Database: PDB / ID: 3f97
TitleCrystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by soman
ComponentsPlatelet-activating factor acetylhydrolase
KeywordsHYDROLASE / PLASMA PLATELET-ACTIVATING FACTOR ACETYLHYDROLASE / SECRETED PROTEIN / ALPHA/BETA-HYDROLASE-FOLD / LDL-BOUND / LIPOPROTEIN ASSOCIATED PHOSPHOLIPASE A2 / LP-PLA2 / GROUP VIIA PLA2 / GLYCOPROTEIN / LIPID DEGRADATION / POLYMORPHISM / SOMAN / Disease mutation / Secreted
Function / homology
Function and homology information


plasma lipoprotein particle oxidation / platelet activating factor catabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling ...plasma lipoprotein particle oxidation / platelet activating factor catabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase / platelet activating factor metabolic process / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase activity / lipid oxidation / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of monocyte chemotaxis / hydrolase activity, acting on ester bonds / phosphatidylcholine catabolic process / peptide hormone processing / Synthesis, secretion, and deacylation of Ghrelin / phospholipid binding / positive regulation of inflammatory response / extracellular region
Similarity search - Function
Platelet-activating factor acetylhydrolase, eucaryote / Platelet-activating factor acetylhydrolase, isoform II / Lipases, serine active site. / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE / Platelet-activating factor acetylhydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSamanta, U. / Bahnson, B.J.
CitationJournal: Biochem Pharmacol / Year: 2009
Title: Crystal structures of human group-VIIA phospholipase A2 inhibited by organophosphorus nerve agents exhibit non-aged complexes.
Authors: Samanta, U. / Kirby, S.D. / Srinivasan, P. / Cerasoli, D.M. / Bahnson, B.J.
History
DepositionNov 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Platelet-activating factor acetylhydrolase
B: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5908
Polymers86,9892
Non-polymers6026
Water7,008389
1
A: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6592
Polymers43,4941
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9326
Polymers43,4941
Non-polymers4375
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.084, 82.697, 96.692
Angle α, β, γ (deg.)90.00, 115.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Platelet-activating factor acetylhydrolase / PAF acetylhydrolase / PAF 2-acylhydrolase / LDL-associated phospholipase A2 / LDL-PLA(2) / 2-acetyl- ...PAF acetylhydrolase / PAF 2-acylhydrolase / LDL-associated phospholipase A2 / LDL-PLA(2) / 2-acetyl-1-alkylglycerophosphocholine esterase / 1-alkyl-2-acetylglycerophosphocholine esterase


Mass: 43494.367 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 47-429
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G7, PAFAH / Production host: Escherichia coli (E. coli)
References: UniProt: Q13093, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Chemical ChemComp-GD7 / (1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE


Mass: 164.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H17O2P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


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


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PH 6.6, pH 6.60, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2006 / Details: ROSENBAUM-ROCK
RadiationMonochromator: SI(111) 0.990 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 87071 / Num. obs: 87071 / % possible obs: 96.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.97
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.36 / % possible all: 73.1

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPOF CCP4Iphasing
REFMACOF CCP4I FOR REFINEMENTrefinement
HKL-2000data reduction
HKL-2000data scaling
REFMACOF CCP4I FOR REFINEMENTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NATIVE STRUCTURE, PDB ENTRY 3D59

3d59


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / SU B: 1.768 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.107 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21197 4376 5 %RANDOM
Rwork0.1817 ---
obs0.18321 82693 96.2 %-
all-87071 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20.23 Å2
2--0.88 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6016 0 53 389 6458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226209
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.9598406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35623.986296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.946151083
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2571536
X-RAY DIFFRACTIONr_chiral_restr0.0950.2913
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024666
X-RAY DIFFRACTIONr_nbd_refined0.2190.22985
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2429
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.227
X-RAY DIFFRACTIONr_mcbond_it0.9151.53794
X-RAY DIFFRACTIONr_mcangle_it1.55225987
X-RAY DIFFRACTIONr_scbond_it2.31832723
X-RAY DIFFRACTIONr_scangle_it3.6184.52419
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 233 -
Rwork0.209 4307 -
obs--68.04 %

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