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- PDB-7mt1: Crystal structure of Human Platelet-activating factor acetylhydro... -

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Basic information

Entry
Database: PDB / ID: 7mt1
TitleCrystal structure of Human Platelet-activating factor acetylhydrolase IB subunit beta (PAFAH1B1)
ComponentsPlatelet-activating factor acetylhydrolase IB subunit beta
KeywordsPROTEIN BINDING / PAFAH1B1 / WD40 / WD-repeat protein / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


corpus callosum morphogenesis / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / interneuron migration / maintenance of centrosome location / platelet activating factor metabolic process / radial glia-guided pyramidal neuron migration / acrosome assembly ...corpus callosum morphogenesis / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / establishment of planar polarity of embryonic epithelium / 1-alkyl-2-acetylglycerophosphocholine esterase complex / interneuron migration / maintenance of centrosome location / platelet activating factor metabolic process / radial glia-guided pyramidal neuron migration / acrosome assembly / cerebral cortex neuron differentiation / central region of growth cone / establishment of centrosome localization / microtubule sliding / positive regulation of embryonic development / positive regulation of cytokine-mediated signaling pathway / microtubule organizing center organization / layer formation in cerebral cortex / auditory receptor cell development / nuclear membrane disassembly / astral microtubule / cortical microtubule organization / positive regulation of dendritic spine morphogenesis / vesicle transport along microtubule / myeloid leukocyte migration / reelin-mediated signaling pathway / stereocilium / osteoclast development / microtubule plus-end binding / stem cell division / brain morphogenesis / negative regulation of JNK cascade / COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport / kinesin complex / microtubule associated complex / motile cilium / dynein intermediate chain binding / nuclear migration / cochlea development / dynein complex binding / transmission of nerve impulse / cell leading edge / phospholipase binding / germ cell development / establishment of mitotic spindle orientation / dynactin binding / neuromuscular process controlling balance / protein secretion / neuroblast proliferation / positive regulation of axon extension / microtubule-based process / cytoplasmic microtubule / lipid catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / JNK cascade / axon cytoplasm / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of mitotic cell cycle / regulation of microtubule cytoskeleton organization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / adult locomotory behavior / hippocampus development / AURKA Activation by TPX2 / phosphoprotein binding / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / cerebral cortex development / kinetochore / microtubule cytoskeleton organization / neuron migration / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / heparin binding / negative regulation of neuron projection development / actin cytoskeleton organization / cell cortex / microtubule binding / chemical synaptic transmission / nuclear membrane / learning or memory / neuron projection / protein heterodimerization activity / neuronal cell body / centrosome / perinuclear region of cytoplasm / glutamatergic synapse / extracellular exosome / identical protein binding / cytosol
Similarity search - Function
: / LisH / Dynein regulator LIS1 / LIS1, N-terminal / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. ...: / LisH / Dynein regulator LIS1 / LIS1, N-terminal / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Platelet-activating factor acetylhydrolase IB subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsHutchinson, A. / Seitova, A. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC)
CitationJournal: To Be Published
Title: Crystal structure of Human Platelet-activating factor acetylhydrolase IB subunit beta (PAFAH1B1)
Authors: Hutchinson, A. / Seitova, A. / Dong, A. / Loppnau, P. / Edwards, A.M. / Arrowsmith, C.H. / Halabelian, L. / Structural Genomics Consortium (SGC)
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)39,1066
Polymers39,0141
Non-polymers925
Water4,522251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.728, 68.572, 69.549
Angle α, β, γ (deg.)90.000, 101.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Platelet-activating factor acetylhydrolase IB subunit beta / Lissencephaly-1 protein / LIS-1 / PAF acetylhydrolase 45 kDa subunit / PAF-AH 45 kDa subunit / PAF- ...Lissencephaly-1 protein / LIS-1 / PAF acetylhydrolase 45 kDa subunit / PAF-AH 45 kDa subunit / PAF-AH alpha / PAFAH alpha


Mass: 39014.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PAFAH1B1, LIS1, MDCR, MDS, PAFAHA / Plasmid: pFBOH-MHL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43034
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 4 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.2 Å3/Da / Density % sol: 44.13 % / Mosaicity: 0.09 °
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 18% PEG8K, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.3→36.04 Å / Num. obs: 82396 / % possible obs: 99.2 % / Redundancy: 5.6 % / CC1/2: 1 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.015 / Rrim(I) all: 0.037 / Net I/σ(I): 22.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.3-1.325.30.4772034538660.8620.2280.5313.194.4
7.12-36.025.60.02129895330.9990.0090.02365.898.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vyh

1vyh


Resolution: 1.3→36.03 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.728 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 3953 4.8 %RANDOM
Rwork0.1766 ---
obs0.1775 78418 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 73.33 Å2 / Biso mean: 15.789 Å2 / Biso min: 8.26 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.24 Å2
2--0.34 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 1.3→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 10 258 2733
Biso mean--33.66 28.87 -
Num. residues----314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132638
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172375
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.6373595
X-RAY DIFFRACTIONr_angle_other_deg1.3761.5765517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8235337
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.90721.308130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.7115444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7481517
X-RAY DIFFRACTIONr_chiral_restr0.0690.2345
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022984
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 288 -
Rwork0.28 5572 -
all-5860 -
obs--96.18 %

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