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- PDB-3dt6: Crystal Structure of Bovin Brain Platelet Activating Factor Acety... -

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Basic information

Entry
Database: PDB / ID: 3dt6
TitleCrystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Paraoxon
ComponentsBrain Platelet-activating factor acetylhydrolase IB subunit alpha
KeywordsHYDROLASE / PLATELET ACTIVATING FACTOR ACETYLHYDROLASE / PAF-AH IB / ALPHA-1 SUBUNIT / LIS1 / GROUP VIII PHOSPHOLIPASE A2 / 26 kDa / PARAOXON / Cytoplasm / 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 / 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
DIETHYL PHOSPHONATE / Platelet-activating factor acetylhydrolase IB subunit alpha1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsEpstein, T.M. / Samanta, U. / Bahnson, B.J.
Citation
Journal: Biochemistry / Year: 2009
Title: Crystal structures of brain group-VIII phospholipase A2 in nonaged complexes with the organophosphorus nerve agents soman and sarin.
Authors: Epstein, T.M. / Samanta, U. / Kirby, S.D. / Cerasoli, D.M. / Bahnson, B.J.
#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
DepositionJul 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Brain Platelet-activating factor acetylhydrolase IB subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0252
Polymers25,8871
Non-polymers1381
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.270, 81.270, 72.506
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 Brain Platelet-activating factor acetylhydrolase IB subunit alpha / PAF acetylhydrolase 29 kDa subunit / PAF-AH 29 kDa subunit / PAF-AH subunit alpha / PAFAH subunit alpha


Mass: 25887.297 Da / Num. of mol.: 1 / Mutation: C55S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PAFAH1B3, PAFAHG / Organ: BRAIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 24, 2003 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→70.36 Å / Num. all: 15253 / Num. obs: 15253 / % possible obs: 92.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 28.28
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.3 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMACOF CCP4I FOR FINAL REFINEMENTrefinement
CNSrefinement
CrystalCleardata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
REFMACOF CCP4I FOR FINAL REFINEMENTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WAB

1wab


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.251 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.215 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20559 754 5.1 %RANDOM
Rwork0.19926 ---
obs0.19957 13973 89.03 %-
all-13973 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.629 Å2
Baniso -1Baniso -2Baniso -3
1--0.88 Å2-0.44 Å20 Å2
2---0.88 Å20 Å2
3---1.32 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1609 0 8 82 1699
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211662
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3631.9412275
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7845211
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.423.97373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26415239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2158
X-RAY DIFFRACTIONr_chiral_restr0.0990.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021284
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.2752
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21121
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.281
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0940.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3671.51088
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.75321691
X-RAY DIFFRACTIONr_scbond_it2.5743651
X-RAY DIFFRACTIONr_scangle_it3.8164.5584
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 64 -
Rwork0.252 912 -
obs--81.4 %

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