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Yorodumi- PDB-8fut: Crystal structure of Xenopus laevis arrestin 1 - P3121 crystal form -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fut | ||||||||||||
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Title | Crystal structure of Xenopus laevis arrestin 1 - P3121 crystal form | ||||||||||||
Components | S-arrestin | ||||||||||||
Keywords | SIGNALING PROTEIN / arrestin 1 / visual arrestin / S-antigen | ||||||||||||
Function / homology | Function and homology information G protein-coupled receptor internalization / photoreceptor outer segment / visual perception / photoreceptor inner segment / G protein-coupled receptor binding / signal transduction / membrane Similarity search - Function | ||||||||||||
Biological species | Xenopus laevis (African clawed frog) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.54 Å | ||||||||||||
Authors | Salom, D. / Barnes, C.L. / Calvert, P.D. / Kiser, P.D. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: To Be Published Title: Crystal structure of Xenopus laevis arrestin 1 - P3121 crystal form Authors: Salom, D. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fut.cif.gz | 86.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fut.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 8fut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8fut_validation.pdf.gz | 419.5 KB | Display | wwPDB validaton report |
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Full document | 8fut_full_validation.pdf.gz | 421.5 KB | Display | |
Data in XML | 8fut_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 8fut_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/8fut ftp://data.pdbj.org/pub/pdb/validation_reports/fu/8fut | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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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: 44685.699 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: sag / Production host: Escherichia coli (E. coli) / References: UniProt: P51477 |
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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: 3.02 Å3/Da / Density % sol: 59.27 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 140 mM ammonium chloride 70 mM HEPES, pH 7.5 17.5 % glycerol ethoxylate 6 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→50 Å / Num. obs: 18443 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.148 / Net I/σ(I): 13.47 |
Reflection shell | Resolution: 2.54→2.69 Å / Rmerge(I) obs: 3.361 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2861 / CC1/2: 0.393 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.54→49.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.847 / SU ML: 0.222 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.753 Å2
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Refinement step | Cycle: 1 / Resolution: 2.54→49.73 Å
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