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- PDB-3f98: Crystal structure of human plasma platelet activating factor acet... -

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Basic information

Entry
Database: PDB / ID: 3f98
TitleCrystal structure of human plasma platelet activating factor acetylhydrolase covalently inhibited by tabun
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 / TABUN / 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 / 1-alkyl-2-acetylglycerophosphocholine esterase activity / platelet activating factor metabolic process / 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 / calcium-independent phospholipase A2 activity / 1-alkyl-2-acetylglycerophosphocholine esterase activity / platelet activating factor metabolic process / lipid oxidation / low-density lipoprotein particle / high-density lipoprotein particle / low-density lipoprotein particle remodeling / positive regulation of monocyte chemotaxis / phosphatidylcholine catabolic process / 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
FORMIC ACID / R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE / 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_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 1.3Nov 20, 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
C: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,85392
Polymers130,4833
Non-polymers4,37089
Water19,5281084
1
A: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,05833
Polymers43,4941
Non-polymers1,56432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,87429
Polymers43,4941
Non-polymers1,38028
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Platelet-activating factor acetylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,92030
Polymers43,4941
Non-polymers1,42629
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.984, 133.322, 253.855
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1356-

HOH

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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.: 3 / 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-NTJ / R-ETHYL N,N-DIMETHYLPHOSPHONAMIDATE


Mass: 137.117 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO2P
#3: Chemical...
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 86 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1084 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0055 / Wavelength: 1.0055 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 12, 2006 / Details: ROSENBAUM-ROCK
RadiationMonochromator: SI(111) 0.990 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0055 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 141507 / Num. obs: 141507 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 35.025
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.435 / Mean I/σ(I) obs: 5.59 / % possible all: 97.8

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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: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.692 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.106 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20165 7097 5 %RANDOM
Rwork0.17894 ---
obs0.18008 134355 98.81 %-
all-141507 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.122 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.04 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9351 0 24 1342 10717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229772
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.95813072
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.551126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8323.941472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.629151737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9311560
X-RAY DIFFRACTIONr_chiral_restr0.0990.21425
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027204
X-RAY DIFFRACTIONr_nbd_refined0.2210.25137
X-RAY DIFFRACTIONr_nbtor_refined0.3090.26633
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.21135
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.2183
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.275
X-RAY DIFFRACTIONr_mcbond_it0.8871.55995
X-RAY DIFFRACTIONr_mcangle_it1.45629246
X-RAY DIFFRACTIONr_scbond_it1.94134267
X-RAY DIFFRACTIONr_scangle_it2.9454.53826
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 497 -
Rwork0.189 9769 -
obs--97.82 %

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