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- PDB-3dt9: Crystal Structure of Bovin Brain Platelet Activating Factor Acety... -

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Basic information

Entry
Database: PDB / ID: 3dt9
TitleCrystal Structure of Bovin Brain Platelet Activating Factor Acetylhydrolase Covalently Inhibited by Soman
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 / SOMAN / Cytoplasm / Lipid degradation / PLATELET FACTOR
Function / homology
Function and homology information


platelet-activating factor acetyltransferase activity / 1-alkyl-2-acetylglycerophosphocholine esterase complex / 1-alkyl-2-acetylglycerophosphocholine esterase / COPI-independent Golgi-to-ER retrograde traffic / 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
(1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE / Platelet-activating factor acetylhydrolase IB subunit alpha1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 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
Revision 1.6Nov 6, 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: Brain Platelet-activating factor acetylhydrolase IB subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0512
Polymers25,8871
Non-polymers1641
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.356, 81.356, 72.969
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 (domestic cattle) / Gene: PAFAH1B3, PAFAHG / Organ: BRAIN / Production host: Escherichia coli (E. coli)
References: UniProt: Q29460, 1-alkyl-2-acetylglycerophosphocholine esterase
#2: Chemical ChemComp-GD7 / (1R)-1,2,2-TRIMETHYLPROPYL (R)-METHYLPHOSPHINATE


Mass: 164.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17O2P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, Sodium acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Sep 5, 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: 1.85→70.53 Å / Num. all: 23397 / Num. obs: 23397 / % possible obs: 96.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 23.44
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.451 / Mean I/σ(I) obs: 2.51 / % possible all: 88.9

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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: 1.85→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.347 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.142 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22831 1157 5.1 %RANDOM
Rwork0.21031 ---
obs0.2112 21324 92.82 %-
all-21324 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.544 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.11 Å20 Å2
2---0.23 Å20 Å2
3---0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 10 80 1755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211719
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9472342
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1035209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.37923.04982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35115269
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4341514
X-RAY DIFFRACTIONr_chiral_restr0.0950.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021320
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2460.2825
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21161
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.286
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.223
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0840.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3211.51084
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.64921696
X-RAY DIFFRACTIONr_scbond_it2.5173710
X-RAY DIFFRACTIONr_scangle_it3.7834.5646
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 66 -
Rwork0.266 1300 -
obs--77.53 %

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