+Open data
-Basic information
Entry | Database: PDB / ID: 3ayn | ||||||
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Title | Crystal structure of squid isorhodopsin | ||||||
Components | Rhodopsin | ||||||
Keywords | SIGNALING PROTEIN / transmembrane protein / Photoreceptor / Chromophore / Glycoprotein / Lipoprotein / Gq-type G-protein / Phosphorylation / membrane | ||||||
Function / homology | Function and homology information retinal binding / photoreceptor activity / phototransduction / visual perception / cell projection / G protein-coupled receptor activity / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Todarodes pacificus (Japanese flying squid) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Murakami, M. / Kouyama, T. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystallographic Analysis of the Primary Photochemical Reaction of Squid Rhodopsin Authors: Murakami, M. / Kouyama, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ayn.cif.gz | 148.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ayn.ent.gz | 121.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ayn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ay/3ayn ftp://data.pdbj.org/pub/pdb/validation_reports/ay/3ayn | HTTPS FTP |
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-Related 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
-Protein / Sugars , 2 types, 3 molecules AB
#1: Protein | Mass: 49872.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) Todarodes pacificus (Japanese flying squid) References: UniProt: P31356 #6: Sugar | ChemComp-BOG / | |
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-Non-polymers , 5 types, 66 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / | #5: Chemical | ChemComp-PC1 / | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.29 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 3.2M ammonium sulfate, 20mM MES, 50mM EDTA, 10mM beta-mercaptoethanol , pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 21, 2010 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→61.26 Å / Num. obs: 36893 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5389 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→15 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 1907373.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 74.9602 Å2 | ||||||||||||||||||||
Displacement parameters | Biso max: 139.5 Å2 / Biso mean: 55.9608 Å2 / Biso min: 20 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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