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Yorodumi- PDB-7o7h: Crystal structure of rsEGFP2 mutant V151L in the non-fluorescent ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7o7h | ||||||
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Title | Crystal structure of rsEGFP2 mutant V151L in the non-fluorescent off-state determined by synchrotron radiation at 100K | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / Reversibly photoswitchable fluorescent protein | ||||||
Function / homology | Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / bioluminescence / generation of precursor metabolites and energy / Green fluorescent protein Function and homology information | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Woodhouse, J. / Adam, V. / Hadjidemetriou, K. / Colletier, J.P. / Weik, M. | ||||||
Citation | Journal: Chemphyschem / Year: 2022 Title: Rational Control of Off-State Heterogeneity in a Photoswitchable Fluorescent Protein Provides Switching Contrast Enhancement. Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / ...Authors: Adam, V. / Hadjidemetriou, K. / Jensen, N. / Shoeman, R.L. / Woodhouse, J. / Aquila, A. / Banneville, A.S. / Barends, T.R.M. / Bezchastnov, V. / Boutet, S. / Byrdin, M. / Cammarata, M. / Carbajo, S. / Eleni Christou, N. / Coquelle, N. / De la Mora, E. / El Khatib, M. / Moreno Chicano, T. / Bruce Doak, R. / Fieschi, F. / Foucar, L. / Glushonkov, O. / Gorel, A. / Grunbein, M.L. / Hilpert, M. / Hunter, M. / Kloos, M. / Koglin, J.E. / Lane, T.J. / Liang, M. / Mantovanelli, A. / Nass, K. / Nass Kovacs, G. / Owada, S. / Roome, C.M. / Schiro, G. / Seaberg, M. / Stricker, M. / Thepaut, M. / Tono, K. / Ueda, K. / Uriarte, L.M. / You, D. / Zala, N. / Domratcheva, T. / Jakobs, S. / Sliwa, M. / Schlichting, I. / Colletier, J.P. / Bourgeois, D. / Weik, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7o7h.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7o7h.ent.gz | 55.5 KB | Display | PDB format |
PDBx/mmJSON format | 7o7h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/7o7h ftp://data.pdbj.org/pub/pdb/validation_reports/o7/7o7h | HTTPS FTP |
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-Related structure data
Related structure data | 7ambC 7amfC 7o7cC 7o7dC 7o7eC 7o7uC 7o7vC 7o7wC 7o7xC 5dtxS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28546.230 Da / Num. of mol.: 1 Mutation: M1_S2insV, F64L, S65T, H231L, A206K, Q69L, V163S, T65A, V150L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.93 Å3/Da / Density % sol: 36.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 1.8 M ammonium sulfate, 100 mM HEPES pH 8.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→46.16 Å / Num. obs: 84740 / % possible obs: 97.2 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rrim(I) all: 0.047 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.7→1.81 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.9 / Num. unique obs: 2539 / CC1/2: 0.871 / Rrim(I) all: 42.8 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DTX Resolution: 1.7→46.16 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.64 / 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: 92.83 Å2 / Biso mean: 31.4697 Å2 / Biso min: 13.96 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→46.16 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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