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- PDB-7mp1: CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1,5... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7mp1 | ||||||
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Title | CRYSTAL STRUCTURE OF NATIVE BOVINE ARRESTIN 1 IN COMPLEX WITH 1,5-DI-METHYLENEBISPHOSPHONATE INOSITOL TETRAKISPHOSPHATE (1,5-PCP-IP4) | ||||||
![]() | S-arrestin | ||||||
![]() | PROTEIN BINDING / GPCR / rhodopsin / phototransduction / inositol / 5PP-IP5 / IP7 | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sander, C.L. / Palczewski, K. / Kiser, P.D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural evidence for visual arrestin priming via complexation of phosphoinositols. Authors: Sander, C.L. / Luu, J. / Kim, K. / Furkert, D. / Jang, K. / Reichenwallner, J. / Kang, M. / Lee, H.J. / Eger, B.T. / Choe, H.W. / Fiedler, D. / Ernst, O.P. / Kim, Y.J. / Palczewski, K. / Kiser, P.D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 298.2 KB | Display | ![]() |
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PDB format | ![]() | 242.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 50.6 KB | Display | |
Data in CIF | ![]() | 67.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7f1wC ![]() 7f1xC ![]() 7jsmC ![]() 7jtbSC ![]() 7jxaC ![]() 7morC ![]() 7mp0C ![]() 7mp2C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / Refine code: _
NCS ensembles :
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Components
#1: Protein | Mass: 45334.781 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: Chemical | ChemComp-4WZ / {[( #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.95 Å3/Da / Density % sol: 68.83 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.1 M Bis-Tris propane pH 7.0, 35% 2-Ethoxyethanol, 0.001 M Magnesium acetate, 5 mM 1,5-DI-METHYLENEBISPHOSPHONATE INOSITOL TETRAKISPHOSPHATE (1,5-PCP-IP4) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→50 Å / Num. obs: 83087 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 77.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Net I/σ(I): 16.07 |
Reflection shell | Resolution: 2.66→2.82 Å / Rmerge(I) obs: 2.77 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 13219 / CC1/2: 0.532 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7JTB Resolution: 2.66→49.23 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 13.13 / SU ML: 0.238 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.363 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 231.67 Å2 / Biso mean: 86.133 Å2 / Biso min: 38.01 Å2
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Refinement step | Cycle: final / Resolution: 2.66→49.23 Å
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Refine LS restraints |
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Refine LS restraints NCS | Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05
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LS refinement shell | Resolution: 2.66→2.729 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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