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Yorodumi- PDB-5zih: Crystal structure of the red light-activated channelrhodopsin Chr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5zih | |||||||||
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Title | Crystal structure of the red light-activated channelrhodopsin Chrimson. | |||||||||
Components | Sensory opsin A,Chrimson | |||||||||
Keywords | MEMBRANE PROTEIN / rhodopsin / ion channel | |||||||||
Function / homology | Bacteriorhodopsin-like protein / Archaeal/bacterial/fungal rhodopsins / Bacteriorhodopsin-like protein / membrane / metal ion binding / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Sensory opsin A Function and homology information | |||||||||
Biological species | Chlamydomonas reinhardtii (plant) Chlamydomonas noctigama (plant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Oda, K. / Vierock, J. / Oishi, S. / Taniguchi, R. / Yamashita, K. / Nishizawa, T. / Hegemann, P. / Nureki, O. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: Nat Commun / Year: 2018 Title: Crystal structure of the red light-activated channelrhodopsin Chrimson. Authors: Oda, K. / Vierock, J. / Oishi, S. / Rodriguez-Rozada, S. / Taniguchi, R. / Yamashita, K. / Wiegert, J.S. / Nishizawa, T. / Hegemann, P. / Nureki, O. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5zih.cif.gz | 137.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5zih.ent.gz | 106.6 KB | Display | PDB format |
PDBx/mmJSON format | 5zih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5zih_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 5zih_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 5zih_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 5zih_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/5zih ftp://data.pdbj.org/pub/pdb/validation_reports/zi/5zih | HTTPS FTP |
-Related structure data
Related structure data | 3ug9S S: Starting model for refinement |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.5281/zenodo.1319974 / Data set type: diffraction image data / Metadata reference: 10.5281/zenodo.1319974 |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38959.156 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Chrimson with substituted N-terminal CrChR1 sequence Source: (gene. exp.) Chlamydomonas reinhardtii (plant), (gene. exp.) Chlamydomonas noctigama (plant) Gene: CSOA / Plasmid: pFastBac1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q8L435 #2: Chemical | ChemComp-OLC / ( #3: 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: 2.73 Å3/Da / Density % sol: 54.95 % |
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Crystal grow | Temperature: 298 K / Method: lipidic cubic phase / pH: 7 / Details: PEG500DME, Na citrate, Na malonate, sarcosine |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 23, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 30180 / % possible obs: 100 % / Redundancy: 9.3 % / Biso Wilson estimate: 24.96 Å2 / CC1/2: 0.98 / Rrim(I) all: 0.144 / Χ2: 1.237 / Net I/σ(I): 13.8 / Num. measured all: 276798 / Scaling rejects: 214 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 9.2 % / Mean I/σ(I) obs: 1.7 / Num. measured obs: 41376 / Num. possible: 4768 / Num. unique obs: 4767 / CC1/2: 0.595 / Rrim(I) all: 0.591 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3UG9 Resolution: 2.6→48.818 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.76 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.21 Å2 / Biso mean: 38.6213 Å2 / Biso min: 3.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.6→48.818 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19
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