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- PDB-3f9c: Crystal structure of human plasma platelet activating factor acet... -

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Basic information

Entry
Database: PDB / ID: 3f9c
TitleCrystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by diisopropylfluorophosphate
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 / DIISOPROPYLFLUOROPHOSPHATE / DFP / Disease mutation / Secreted
Function / homology
Function and homology information


plasma lipoprotein particle oxidation / platelet activating factor catabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase / calcium-independent phospholipase A2 activity / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine catabolic process / lipid oxidation / low-density lipoprotein particle / high-density lipoprotein particle ...plasma lipoprotein particle oxidation / platelet activating factor catabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase / calcium-independent phospholipase A2 activity / platelet activating factor metabolic process / 1-alkyl-2-acetylglycerophosphocholine esterase activity / phosphatidylcholine catabolic process / lipid oxidation / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of monocyte chemotaxis / peptide hormone processing / hydrolase activity, acting on ester bonds / 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
DIISOPROPYL PHOSPHONATE / Platelet-activating factor acetylhydrolase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 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)87,3214
Polymers86,9892
Non-polymers3322
Water3,063170
1
A: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6612
Polymers43,4941
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6612
Polymers43,4941
Non-polymers1661
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)116.375, 82.400, 96.511
Angle α, β, γ (deg.)90.00, 115.64, 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-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 48.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PH 6.6. NATIVE PROTEIN CRYSTAL SOAKED IN MOTHER LIQUOR CONTAINING DFP, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: May 15, 2008 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 36675 / Num. obs: 36675 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.71
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.23 / % possible all: 100

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Processing

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

3d59


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 7.754 / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.358 / ESU R Free: 0.257 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26109 1826 5 %RANDOM
Rwork0.19595 ---
obs0.19919 34789 99.94 %-
all-36675 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.908 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å20 Å20.46 Å2
2--0.56 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5978 0 20 170 6168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226142
X-RAY DIFFRACTIONr_angle_refined_deg1.8131.9538301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8235739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.30223.966295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.355151061
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3551536
X-RAY DIFFRACTIONr_chiral_restr0.1190.2891
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024654
X-RAY DIFFRACTIONr_nbd_refined0.2310.22823
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24082
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2312
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3520.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.27
X-RAY DIFFRACTIONr_mcbond_it1.0581.53816
X-RAY DIFFRACTIONr_mcangle_it1.75225944
X-RAY DIFFRACTIONr_scbond_it2.5932693
X-RAY DIFFRACTIONr_scangle_it3.8254.52357
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 121 -
Rwork0.245 2542 -
obs--99.78 %

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