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- PDB-5tuc: Crystal Structure of the Sus TBC1D15 GAP Domain -

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Basic information

Entry
Database: PDB / ID: 5tuc
TitleCrystal Structure of the Sus TBC1D15 GAP Domain
ComponentsSus TBC1D15 GAP Domain
KeywordsHYDROLASE ACTIVATOR / Sus (Sus scrofa) / TBC1D15 / GAP (GTPase-activating Protein) / GTPase / PROTEIN BINDING
Function / homologySmall G protein signalling modulator 1/2, Rab-binding domain / Rab-binding domain (RBD) / 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. / cytoplasm / TBC1 domain family member 15
Function and homology information
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, Y.-N. / Wang, W. / Cheng, D. / Ge, Y. / Gu, X. / Zhou, X.E. / Ye, F. / Xu, H.E. / Lv, Z.
CitationJournal: Protein Sci. / Year: 2017
Title: Crystal structure of TBC1D15 GTPase-activating protein (GAP) domain and its activity on Rab GTPases.
Authors: Chen, Y.N. / Gu, X. / Zhou, X.E. / Wang, W. / Cheng, D. / Ge, Y. / Ye, F. / Xu, H.E. / Lv, Z.
History
DepositionNov 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Oct 4, 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sus TBC1D15 GAP Domain
B: Sus TBC1D15 GAP Domain


Theoretical massNumber of molelcules
Total (without water)83,1152
Polymers83,1152
Non-polymers00
Water2,774154
1
A: Sus TBC1D15 GAP Domain


Theoretical massNumber of molelcules
Total (without water)41,5581
Polymers41,5581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sus TBC1D15 GAP Domain


Theoretical massNumber of molelcules
Total (without water)41,5581
Polymers41,5581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)139.000, 139.000, 175.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-703-

HOH

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Components

#1: Protein Sus TBC1D15 GAP Domain


Mass: 41557.730 Da / Num. of mol.: 2 / Fragment: UNP residues 270-617
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TBC1D15 / Production host: Escherichia coli (E. coli) / References: UniProt: F1SH24
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.94 Å3/Da / Density % sol: 58.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 50 mM MES sodium Salt (pH 6.5), 20% (w/v) PEG1000, 100 mM sodium chloride and 200 mM magnesium chloride
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 35232 / % possible obs: 100 % / Redundancy: 39.6 % / Rmerge(I) obs: 0.172 / Net I/σ(I): 22.2
Reflection shellResolution: 2.5→2.61 Å / Rmerge(I) obs: 1.254 / Mean I/σ(I) obs: 4.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QFZ

2qfz


Resolution: 2.5→87.62 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2528 2498 7.1 %
Rwork0.2137 --
obs0.2165 35202 99.98 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→87.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5405 0 0 154 5559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045518
X-RAY DIFFRACTIONf_angle_d0.8737420
X-RAY DIFFRACTIONf_dihedral_angle_d12.3832109
X-RAY DIFFRACTIONf_chiral_restr0.034790
X-RAY DIFFRACTIONf_plane_restr0.003942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54810.33941340.29361777X-RAY DIFFRACTION100
2.5481-2.60010.2911380.28251777X-RAY DIFFRACTION100
2.6001-2.65670.29921270.2711793X-RAY DIFFRACTION100
2.6567-2.71850.32381170.26731791X-RAY DIFFRACTION100
2.7185-2.78640.33091280.27241801X-RAY DIFFRACTION100
2.7864-2.86180.30981430.26781768X-RAY DIFFRACTION100
2.8618-2.9460.34121450.27271787X-RAY DIFFRACTION100
2.946-3.04110.31371470.26351792X-RAY DIFFRACTION100
3.0411-3.14980.29371240.24791796X-RAY DIFFRACTION100
3.1498-3.27590.26981240.24771811X-RAY DIFFRACTION100
3.2759-3.4250.29351430.22251805X-RAY DIFFRACTION100
3.425-3.60560.25451300.22281818X-RAY DIFFRACTION100
3.6056-3.83150.23991410.20211805X-RAY DIFFRACTION100
3.8315-4.12730.2121520.17831817X-RAY DIFFRACTION100
4.1273-4.54270.23221460.16761828X-RAY DIFFRACTION100
4.5427-5.19990.21691480.17531851X-RAY DIFFRACTION100
5.1999-6.5510.24671420.20161884X-RAY DIFFRACTION100
6.551-87.67380.17561690.17352003X-RAY DIFFRACTION100

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