+Open data
-Basic information
Entry | Database: PDB / ID: 1ayr | ||||||
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Title | ARRESTIN FROM BOVINE ROD OUTER SEGMENTS | ||||||
Components | ARRESTIN | ||||||
Keywords | SENSORY TRANSDUCTION / ARRESTIN / RHODOPSIN | ||||||
Function / homology | Function and homology information Inactivation, recovery and regulation of the phototransduction cascade / G protein-coupled receptor internalization / photoreceptor outer segment / response to light stimulus / photoreceptor inner segment / G protein-coupled receptor binding / signal transduction / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.3 Å | ||||||
Authors | Granzin, J. / Wilden, U. / Choe, H.-W. / Labahn, J. / Krafft, B. / Bueldt, G. | ||||||
Citation | Journal: Nature / Year: 1998 Title: X-ray crystal structure of arrestin from bovine rod outer segments. Authors: Granzin, J. / Wilden, U. / Choe, H.W. / Labahn, J. / Krafft, B. / Buldt, G. #1: Journal: FEBS Lett. / Year: 1997 Title: Crystallization and Preliminary X-Ray Analysis of Arrestin from Bovine Rod Outer Segment Authors: Wilden, U. / Choe, H.W. / Krafft, B. / Granzin, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ayr.cif.gz | 272.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ayr.ent.gz | 225.1 KB | Display | PDB format |
PDBx/mmJSON format | 1ayr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/1ayr ftp://data.pdbj.org/pub/pdb/validation_reports/ay/1ayr | 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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 41001.273 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: ROD OUTER SEGMENTS / Cellular location: CYTOPLASM / Organ: EYE / Tissue: RETINA / References: UniProt: P08168 #2: Water | ChemComp-HOH / | Compound details | ARRESTIN QUENCHES THE LIGHT-INDUCED ENZYME CASCADE, BINDS TO PHOSPHORYL | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 3.94 Å3/Da / Density % sol: 68.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.2 / Details: pH 7.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1996 / Details: PT COATED TORROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→26.976 Å / Num. obs: 478820 / % possible obs: 95.1 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.075 / Rsym value: 0.172 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 3.3→3.39 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.172 / Mean I/σ(I) obs: 4.3 / Rsym value: 0.172 / % possible all: 79.7 |
Reflection shell | *PLUS % possible obs: 79.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 3.3→130 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUPED, UNRESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: TORSION-ANGLE MOLECULAR DYNAMICS SLOW COOL REFINEMENT
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Displacement parameters | Biso mean: 27.71 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→130 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS + RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.3→3.45 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor obs: 0.254 |