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Yorodumi- PDB-8faf: Unedited Octopus bimaculoides Synaptotagmin 1 C2A at room temperature -
+Open data
-Basic information
Entry | Database: PDB / ID: 8faf | ||||||
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Title | Unedited Octopus bimaculoides Synaptotagmin 1 C2A at room temperature | ||||||
Components | Synaptotagmin | ||||||
Keywords | EXOCYTOSIS / synaptotagmin 1 / C2 domain / RNA-editing | ||||||
Function / homology | Synaptotagmin / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / C2 domain superfamily / membrane / C2 domain-containing protein Function and homology information | ||||||
Biological species | Octopus bimaculoides (California two-spot octopus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | McNeme, S. / Dominguez, M.J. / Birk, M.A. / Rosenthal, J.C. / Sutton, R.B. | ||||||
Funding support | 1items
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Citation | Journal: Cell / Year: 2023 Title: Temperature-dependent RNA editing in octopus extensively recodes the neural proteome. Authors: Birk, M.A. / Liscovitch-Brauer, N. / Dominguez, M.J. / McNeme, S. / Yue, Y. / Hoff, J.D. / Twersky, I. / Verhey, K.J. / Sutton, R.B. / Eisenberg, E. / Rosenthal, J.J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8faf.cif.gz | 90.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8faf.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 8faf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8faf_validation.pdf.gz | 415.7 KB | Display | wwPDB validaton report |
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Full document | 8faf_full_validation.pdf.gz | 416.6 KB | Display | |
Data in XML | 8faf_validation.xml.gz | 7.1 KB | Display | |
Data in CIF | 8faf_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/8faf ftp://data.pdbj.org/pub/pdb/validation_reports/fa/8faf | HTTPS FTP |
-Related structure data
Related structure data | 8famC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15592.720 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Octopus bimaculoides (California two-spot octopus) Gene: OCBIM_22021175mg / Plasmid: p202 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0L8IHK9 |
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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: 2.13 Å3/Da / Density % sol: 42.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: 23% PEG 3350, 100 mM CHES |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 8, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→42.07 Å / Num. obs: 20317 / % possible obs: 82.99 % / Redundancy: 3.2 % / CC1/2: 0.995 / CC star: 0.999 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.6201 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2009 / CC1/2: 0.632 / CC star: 0.88 / % possible all: 41.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→42.07 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.22 / Stereochemistry target values: ML
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Refinement step | Cycle: LAST / Resolution: 1.85→42.07 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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