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- PDB-5tub: Crystal Structure of the Shark TBC1D15 GAP Domain -

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Basic information

Entry
Database: PDB / ID: 5tub
TitleCrystal Structure of the Shark TBC1D15 GAP Domain
ComponentsShark TBC1D15 GTPase-activating Protein
KeywordsHYDROLASE ACTIVATOR / shark (Chiloscyllium plagiosum) / TBC1D15 / GAP (GTPase-activating Protein) / GTPase / PROTEIN BINDING
Function / homologyDomain 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. / GTPase activator activity / Shark TBC1D15 GTPase-activating Protein
Function and homology information
Biological speciesSqualimorphii (fish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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: Shark TBC1D15 GTPase-activating Protein
B: Shark TBC1D15 GTPase-activating Protein
C: Shark TBC1D15 GTPase-activating Protein
D: Shark TBC1D15 GTPase-activating Protein


Theoretical massNumber of molelcules
Total (without water)166,0004
Polymers166,0004
Non-polymers00
Water1,49583
1
A: Shark TBC1D15 GTPase-activating Protein


Theoretical massNumber of molelcules
Total (without water)41,5001
Polymers41,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shark TBC1D15 GTPase-activating Protein


Theoretical massNumber of molelcules
Total (without water)41,5001
Polymers41,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Shark TBC1D15 GTPase-activating Protein


Theoretical massNumber of molelcules
Total (without water)41,5001
Polymers41,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Shark TBC1D15 GTPase-activating Protein


Theoretical massNumber of molelcules
Total (without water)41,5001
Polymers41,5001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)224.790, 149.740, 95.030
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Shark TBC1D15 GTPase-activating Protein


Mass: 41499.898 Da / Num. of mol.: 4 / Fragment: TBC1D15 GAP Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Squalimorphii (fish) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U7Q1Z6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 4.56 Å3/Da / Density % sol: 73.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: 1.35 M ammonium sulfate, 0.09 M BIS-TRIS propane (pH 7.0) and 0.01 M calcium chloride dehydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.85→47.26 Å / Num. obs: 69398 / % possible obs: 100 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.141 / Net I/σ(I): 10.7
Reflection shellResolution: 2.85→2.92 Å / Rmerge(I) obs: 1.165 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TUC

5tuc


Resolution: 2.85→47.26 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2477 4813 6.94 %
Rwork0.2148 --
obs0.2171 69352 99.93 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11148 0 0 83 11231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611406
X-RAY DIFFRACTIONf_angle_d0.98415360
X-RAY DIFFRACTIONf_dihedral_angle_d11.6684326
X-RAY DIFFRACTIONf_chiral_restr0.041628
X-RAY DIFFRACTIONf_plane_restr0.0041944
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.88240.35531630.33812134X-RAY DIFFRACTION100
2.8824-2.91630.36081400.3212166X-RAY DIFFRACTION100
2.9163-2.95180.35181470.31972147X-RAY DIFFRACTION100
2.9518-2.98920.38791600.32262133X-RAY DIFFRACTION100
2.9892-3.02850.35331730.32742110X-RAY DIFFRACTION100
3.0285-3.070.38231490.33362201X-RAY DIFFRACTION100
3.07-3.11390.37161730.30162098X-RAY DIFFRACTION100
3.1139-3.16030.34241420.30622167X-RAY DIFFRACTION100
3.1603-3.20970.30991370.2772149X-RAY DIFFRACTION100
3.2097-3.26230.30981580.28632170X-RAY DIFFRACTION100
3.2623-3.31860.32181690.28552142X-RAY DIFFRACTION100
3.3186-3.37890.30371700.27562118X-RAY DIFFRACTION100
3.3789-3.44390.28891450.27392147X-RAY DIFFRACTION100
3.4439-3.51410.34311690.2582154X-RAY DIFFRACTION100
3.5141-3.59050.28241700.25652119X-RAY DIFFRACTION100
3.5905-3.6740.27811640.24552174X-RAY DIFFRACTION100
3.674-3.76580.30351560.24632139X-RAY DIFFRACTION100
3.7658-3.86760.26681460.21852190X-RAY DIFFRACTION100
3.8676-3.98140.25671860.21012106X-RAY DIFFRACTION100
3.9814-4.10980.20911710.18712156X-RAY DIFFRACTION100
4.1098-4.25660.24141630.19192122X-RAY DIFFRACTION100
4.2566-4.42690.24241450.1912187X-RAY DIFFRACTION100
4.4269-4.62820.20361500.17882151X-RAY DIFFRACTION100
4.6282-4.8720.20521700.17252149X-RAY DIFFRACTION100
4.872-5.17690.20921350.16752194X-RAY DIFFRACTION100
5.1769-5.5760.23751780.19022146X-RAY DIFFRACTION100
5.576-6.13610.23771620.19822164X-RAY DIFFRACTION100
6.1361-7.02150.19861530.19622171X-RAY DIFFRACTION100
7.0215-8.83690.19321860.16912163X-RAY DIFFRACTION100
8.8369-47.26680.17251830.15782172X-RAY DIFFRACTION99

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