+Open data
-Basic information
Entry | Database: PDB / ID: 5tub | ||||||
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Title | Crystal Structure of the Shark TBC1D15 GAP Domain | ||||||
Components | Shark TBC1D15 GTPase-activating Protein | ||||||
Keywords | HYDROLASE ACTIVATOR / shark (Chiloscyllium plagiosum) / TBC1D15 / GAP (GTPase-activating Protein) / GTPase / PROTEIN BINDING | ||||||
Function / homology | 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. / Shark TBC1D15 GTPase-activating Protein Function and homology information | ||||||
Biological species | Squalimorphii (fish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Chen, Y.-N. / Wang, W. / Cheng, D. / Ge, Y. / Gu, X. / Zhou, X.E. / Ye, F. / Xu, H.E. / Lv, Z. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5tub.cif.gz | 279.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5tub.ent.gz | 228.1 KB | Display | PDB format |
PDBx/mmJSON format | 5tub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/5tub ftp://data.pdbj.org/pub/pdb/validation_reports/tu/5tub | HTTPS FTP |
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-Related structure data
Related structure data | 5tucSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.56 Å3/Da / Density % sol: 73.01 % |
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Crystal grow | Temperature: 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 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.85→2.92 Å / Rmerge(I) obs: 1.165 / Mean I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.85→47.26 Å
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Refine LS restraints |
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LS refinement shell |
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