+Open data
-Basic information
Entry | Database: PDB / ID: 2oaj | ||||||
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Title | Crystal structure of Sro7 from S. cerevisiae | ||||||
Components | Protein SNI1 | ||||||
Keywords | ENDOCYTOSIS/EXOCYTOSIS / WD40 repeat / beta propeller / ENDOCYTOSIS-EXOCYTOSIS COMPLEX | ||||||
Function / homology | Function and homology information small GTPase binding => GO:0031267 / myosin II binding / Golgi to plasma membrane transport / regulation of exocytosis / mating projection tip / syntaxin binding / small GTPase-mediated signal transduction / establishment of cell polarity / regulation of protein secretion / exocytosis ...small GTPase binding => GO:0031267 / myosin II binding / Golgi to plasma membrane transport / regulation of exocytosis / mating projection tip / syntaxin binding / small GTPase-mediated signal transduction / establishment of cell polarity / regulation of protein secretion / exocytosis / GTPase activator activity / SNARE binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å | ||||||
Authors | Hattendorf, D.A. / Weis, W.I. | ||||||
Citation | Journal: Nature / Year: 2007 Title: Structure of the yeast polarity protein Sro7 reveals a SNARE regulatory mechanism. Authors: Hattendorf, D.A. / Andreeva, A. / Gangar, A. / Brennwald, P.J. / Weis, W.I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oaj.cif.gz | 189 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oaj.ent.gz | 146 KB | Display | PDB format |
PDBx/mmJSON format | 2oaj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oa/2oaj ftp://data.pdbj.org/pub/pdb/validation_reports/oa/2oaj | 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: 100137.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: SNI1, SRO7 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12038 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-NA / |
#4: 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: 2.47 Å3/Da / Density % sol: 50.12 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 40 mM MES pH 6.5, 12% PEG 3350, 200 mM ammonium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0781 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 18, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0781 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→58.3 Å / Num. all: 39646 / Num. obs: 39624 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5728 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SIRAS / Resolution: 2.4→49.12 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2984088.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 29.1789 Å2 / ksol: 0.344724 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.4→49.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.55 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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