+Open data
-Basic information
Entry | Database: PDB / ID: 6ixe | ||||||
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Title | Crystal structure of SeMet apo SH3BP5 (I41) | ||||||
Components | SH3 domain-binding protein 5 | ||||||
Keywords | SIGNALING PROTEIN / Rab11 / GEF / SH3BP5 | ||||||
Function / homology | Function and homology information protein kinase inhibitor activity / guanyl-nucleotide exchange factor activity / cytoplasmic vesicle membrane / SH3 domain binding / nuclear body / intracellular signal transduction / signal transduction / mitochondrion / nucleoplasm / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.35 Å | ||||||
Authors | Goto-Ito, S. / Yamagata, A. / Sato, Y. / Fukai, S. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Life Sci Alliance / Year: 2019 Title: Structural basis of guanine nucleotide exchange for Rab11 by SH3BP5. Authors: Goto-Ito, S. / Morooka, N. / Yamagata, A. / Sato, Y. / Sato, K. / Fukai, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ixe.cif.gz | 53.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ixe.ent.gz | 40.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ixe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ixe ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ixe | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26690.434 Da / Num. of mol.: 1 / Mutation: M167A,R260A,R261A,R262A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SH3BP5, SAB / Production host: Escherichia coli (E. coli) / References: UniProt: O60239 |
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#2: Chemical | ChemComp-SIN / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M succinic acid (pH 7.0), 12% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 3.35→50 Å / Num. obs: 4777 / % possible obs: 96.9 % / Redundancy: 8.2 % / Rsym value: 0.158 / Net I/σ(I): 30 |
Reflection shell | Resolution: 3.35→3.41 Å / Rsym value: 0.357 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.35→38.899 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.6 / Phase error: 42.51 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.35→38.899 Å
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Refine LS restraints |
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LS refinement shell |
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