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Yorodumi- PDB-7atp: 2.0 angstrom structure in complex with Ca of plant Extended Synap... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7atp | ||||||
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Title | 2.0 angstrom structure in complex with Ca of plant Extended Synaptotagmin 1, C2A domain | ||||||
Components | Synaptotagmin-1 | ||||||
Keywords | LIPID BINDING PROTEIN / C2 domain / Beta Sandwich / lipid transport / contact sites | ||||||
Function / homology | Function and homology information lipid transport / endocytosis / endosome membrane / lipid binding / endoplasmic reticulum / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Benavente, J.L. / Albert, A. | ||||||
Citation | Journal: Life Sci Alliance / Year: 2021 Title: The structure and flexibility analysis of the Arabidopsis synaptotagmin 1 reveal the basis of its regulation at membrane contact sites. Authors: Benavente, J.L. / Siliqi, D. / Infantes, L. / Lagartera, L. / Mills, A. / Gago, F. / Ruiz-Lopez, N. / Botella, M.A. / Sanchez-Barrena, M.J. / Albert, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7atp.cif.gz | 82.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7atp.ent.gz | 51.5 KB | Display | PDB format |
PDBx/mmJSON format | 7atp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/7atp ftp://data.pdbj.org/pub/pdb/validation_reports/at/7atp | HTTPS FTP |
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-Related structure data
Related structure data | 7as6C 6ankS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16738.291 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SYT1, SYTA, At2g20990, F26H11.25, F5H14.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9SKR2 | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Chemical | ChemComp-ZN / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-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: 20 % w/v Polyethylene glycol 6,000, 100 mM TRIS pH 8.0 and 10 mM Zinc chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→41.59 Å / Num. obs: 12025 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 55.79 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.1→2.16 Å / Rmerge(I) obs: 1.712 / Num. unique obs: 988 / CC1/2: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ANK Resolution: 2.1→41.59 Å / SU ML: 0.3334 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 39.1463 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 92.23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→41.59 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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