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- PDB-5hjq: Crystal structure of the TBC domain of Skywalker/TBC1D24 from Dro... -

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Basic information

Entry
Database: PDB / ID: 5hjq
TitleCrystal structure of the TBC domain of Skywalker/TBC1D24 from Drosophila melanogaster in complex with inositol(1,4,5)triphosphate
ComponentsLD10117p
KeywordsSIGNALING PROTEIN / TBC / RabGAP
Function / homology
Function and homology information


synaptic vesicle endosomal processing / negative regulation of synaptic vesicle recycling / synaptic vesicle recycling via endosome / vesicle-mediated transport in synapse / neuromuscular synaptic transmission / negative regulation of neurotransmitter secretion / regulation of GTPase activity / GTPase activator activity / neuromuscular junction / terminal bouton ...synaptic vesicle endosomal processing / negative regulation of synaptic vesicle recycling / synaptic vesicle recycling via endosome / vesicle-mediated transport in synapse / neuromuscular synaptic transmission / negative regulation of neurotransmitter secretion / regulation of GTPase activity / GTPase activator activity / neuromuscular junction / terminal bouton / synaptic vesicle membrane / neuron projection development / postsynapse / chemical synaptic transmission / response to oxidative stress / endosome membrane / lipid binding / synapse / nucleus / cytoplasm
Similarity search - Function
TLDc domain profile. / TLDc domain / TLD / domain in TBC and LysM domain containing proteins / Domain in Tre-2, BUB2p, and Cdc16p. Probable Rab-GAPs. / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile.
Similarity search - Domain/homology
D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE / GTPase-activating protein skywalker
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFischer, B. / Paesmans, J. / Versees, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Skywalker-TBC1D24 has a lipid-binding pocket mutated in epilepsy and required for synaptic function.
Authors: Fischer, B. / Luthy, K. / Paesmans, J. / De Koninck, C. / Maes, I. / Swerts, J. / Kuenen, S. / Uytterhoeven, V. / Verstreken, P. / Versees, W.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2016Group: Database references
Revision 1.2Nov 16, 2016Group: Database references
Revision 1.3Jan 24, 2018Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LD10117p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5172
Polymers43,0971
Non-polymers4201
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint1 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.720, 87.720, 97.097
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein LD10117p / Skywalker / isoform A / isoform B / isoform H


Mass: 43096.793 Da / Num. of mol.: 1 / Fragment: TBC domain, residues 1-353
Source method: isolated from a genetically manipulated source
Details: Contains a N-terminal His-Tag / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sky, CG9339, Dmel_CG9339 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9VIH7
#2: Chemical ChemComp-I3P / D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE


Mass: 420.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O15P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 1500, sucinate/phosphate/glycine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.3→39.23 Å / Num. obs: 17353 / % possible obs: 99.4 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 18.18
Reflection shellResolution: 2.3→2.44 Å / Rmerge(I) obs: 0.802

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HJN

5hjn


Resolution: 2.3→39.23 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 36.42
RfactorNum. reflection% reflection
Rfree0.2572 858 4.99 %
Rwork0.23 --
obs0.2314 17209 98.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2308 0 24 30 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042394
X-RAY DIFFRACTIONf_angle_d0.8063254
X-RAY DIFFRACTIONf_dihedral_angle_d14.848878
X-RAY DIFFRACTIONf_chiral_restr0.029363
X-RAY DIFFRACTIONf_plane_restr0.004399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2987-2.44270.34211360.31192574X-RAY DIFFRACTION96
2.4427-2.63120.3331390.28712661X-RAY DIFFRACTION98
2.6312-2.8960.34221370.28192677X-RAY DIFFRACTION98
2.896-3.31480.34131440.2672723X-RAY DIFFRACTION99
3.3148-4.17560.23011470.21972789X-RAY DIFFRACTION100
4.1756-39.23530.21971550.1992927X-RAY DIFFRACTION100

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