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Yorodumi- PDB-6jo0: Crystal structure of the DTS-motif rhodopsin from Phaeocystis glo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jo0 | ||||||
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Title | Crystal structure of the DTS-motif rhodopsin from Phaeocystis globosa virus 12T | ||||||
Components | VirRDTS | ||||||
Keywords | MEMBRANE PROTEIN / microbial type rhodopsin from virus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Phaeocystis globosa virus 12T | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å | ||||||
Authors | Hosaka, T. / Kimura-Someya, T. / Shirouzu, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2019 Title: A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Authors: Needham, D.M. / Yoshizawa, S. / Hosaka, T. / Poirier, C. / Choi, C.J. / Hehenberger, E. / Irwin, N.A.T. / Wilken, S. / Yung, C.M. / Bachy, C. / Kurihara, R. / Nakajima, Y. / Kojima, K. / ...Authors: Needham, D.M. / Yoshizawa, S. / Hosaka, T. / Poirier, C. / Choi, C.J. / Hehenberger, E. / Irwin, N.A.T. / Wilken, S. / Yung, C.M. / Bachy, C. / Kurihara, R. / Nakajima, Y. / Kojima, K. / Kimura-Someya, T. / Leonard, G. / Malmstrom, R.R. / Mende, D.R. / Olson, D.K. / Sudo, Y. / Sudek, S. / Richards, T.A. / DeLong, E.F. / Keeling, P.J. / Santoro, A.E. / Shirouzu, M. / Iwasaki, W. / Worden, A.Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jo0.cif.gz | 120.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jo0.ent.gz | 90.7 KB | Display | PDB format |
PDBx/mmJSON format | 6jo0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jo0_validation.pdf.gz | 839.9 KB | Display | wwPDB validaton report |
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Full document | 6jo0_full_validation.pdf.gz | 846.7 KB | Display | |
Data in XML | 6jo0_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 6jo0_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jo/6jo0 ftp://data.pdbj.org/pub/pdb/validation_reports/jo/6jo0 | HTTPS FTP |
-Related structure data
Related structure data | 5b2nS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 28087.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Phaeocystis globosa virus 12T / Gene: PGAG_00290 / Production host: Escherichia coli (E. coli) / References: UniProt: G8DI69 |
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-Non-polymers , 9 types, 111 molecules
#2: Chemical | ChemComp-RET / | ||||||||||||||
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#3: Chemical | ChemComp-OCT / #4: Chemical | ChemComp-PO4 / | #5: Chemical | ChemComp-HEX / #6: Chemical | ChemComp-D10 / | #7: Chemical | ChemComp-D12 / | #8: Chemical | #9: Chemical | ChemComp-OLB / ( | #10: 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: 2.79 Å3/Da / Density % sol: 55.87 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 5.5 Details: Na-citrate (pH 5.5), 150 mM Na-phosphate, 25% PEG 600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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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: Dec 8, 2016 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.65→45.19 Å / Num. obs: 37658 / % possible obs: 99.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Net I/σ(I): 10.2 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5B2N Resolution: 1.651→42.16 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.83
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 87.63 Å2 / Biso mean: 31.9584 Å2 / Biso min: 17.66 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.651→42.16 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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