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Yorodumi- PDB-6fsf: Crystal structure of the tandem PX-PH-domains of Bem3 from Saccha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fsf | |||||||||
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Title | Crystal structure of the tandem PX-PH-domains of Bem3 from Saccharomyces cerevisiae | |||||||||
Components | GTPase-activating protein BEM3 | |||||||||
Keywords | ENDOCYTOSIS / Bem3 / PX domain / PH domain / phox / pleckstrin homology / phosphatidylinositol phosphates / PIP | |||||||||
Function / homology | Function and homology information : / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / septin ring organization / RHOA GTPase cycle / incipient cellular bud site / cellular bud tip ...: / : / RHOF GTPase cycle / CDC42 GTPase cycle / RHOD GTPase cycle / RHOV GTPase cycle / septin ring organization / RHOA GTPase cycle / incipient cellular bud site / cellular bud tip / mating projection tip / phosphatidylinositol-3-phosphate binding / negative regulation of Rho protein signal transduction / establishment of cell polarity / regulation of GTPase activity / Neutrophil degranulation / GTPase activator activity / positive regulation of GTPase activity / cell cortex / signal transduction / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae S288C (yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | |||||||||
Authors | Ali, I. / Eu, S. / Koch, D. / Bleimling, N. / Goody, R.S. / Mueller, M.P. | |||||||||
Funding support | Germany, 2items
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Citation | Journal: Acta Crystallogr F Struct Biol Commun / Year: 2018 Title: Structure of the tandem PX-PH domains of Bem3 from Saccharomyces cerevisiae. Authors: Ali, I. / Eu, S. / Koch, D. / Bleimling, N. / Goody, R.S. / Muller, M.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fsf.cif.gz | 104.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fsf.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 6fsf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/6fsf ftp://data.pdbj.org/pub/pdb/validation_reports/fs/6fsf | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30739.938 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: BEM3, YPL115C, LPH12C / Production host: Escherichia coli (E. coli) / References: UniProt: P32873 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: reservoir 500 ul 0.1 M PCB pH 7.5-7.7, 17-19% PEG1500; 1ul Bem3 (33-48mg/ml in 20 mM Hepes pH 8.0, 100 mM NaCl, 2mM DTE, 5% glycerol) + 1ul reservoir solution PH range: 7.5-7.7 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98013, 0.97794, 0.97793 | ||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 29, 2014 | ||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.2→42.7 Å / Num. obs: 13566 / % possible obs: 100 % / Redundancy: 10.1 % / Rrim(I) all: 0.047 / Net I/σ(I): 26.7 | ||||||||||||
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 9.76 % / Num. unique obs: 1677 / Rrim(I) all: 1.17 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→42.685 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.94
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→42.685 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 33.6576 Å / Origin y: -16.3613 Å / Origin z: -14.7121 Å
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Refinement TLS group | Selection details: all |