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- PDB-5o8a: Crystal Structure of rsEGFP2 in the non-fluorescent off-state det... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5o8a | ||||||
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Title | Crystal Structure of rsEGFP2 in the non-fluorescent off-state determined by SFX | ||||||
![]() | Green fluorescent protein | ||||||
![]() | FLUORESCENT PROTEIN / photoswitching on state fluorescent state chromophore SFX serial femtosecond crystallography CXI LCLS time resolved crystallography chromohore isomerisation | ||||||
Function / homology | ![]() regulation of viral transcription / virion component => GO:0044423 / bioluminescence / generation of precursor metabolites and energy / host cell cytoplasm / host cell nucleus / structural molecule activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. ...Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, F. / Foucar, L. / Guillon, V. / Hilpert, M. / Hunter, M. / Jakobs, S. / Koglin, J.E. / Kovacsova, G. / Lane, T.J. / Levy, B. / Liang, M. / Nass, K. / Ridard, J. / Robinson, J.S. / Roome, C.M. / Ruckebusch, C. / Seaberg, M. / Thepaut, M. / Cammarata, M. / Demachy, I. / Field, M. / Shoeman, R.L. / Bourgeois, D. / Colletier, J.P. / Schlichting, I. / Weik, M. | ||||||
![]() | ![]() Title: Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography. Authors: Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, ...Authors: Coquelle, N. / Sliwa, M. / Woodhouse, J. / Schiro, G. / Adam, V. / Aquila, A. / Barends, T.R.M. / Boutet, S. / Byrdin, M. / Carbajo, S. / De la Mora, E. / Doak, R.B. / Feliks, M. / Fieschi, F. / Foucar, L. / Guillon, V. / Hilpert, M. / Hunter, M.S. / Jakobs, S. / Koglin, J.E. / Kovacsova, G. / Lane, T.J. / Levy, B. / Liang, M. / Nass, K. / Ridard, J. / Robinson, J.S. / Roome, C.M. / Ruckebusch, C. / Seaberg, M. / Thepaut, M. / Cammarata, M. / Demachy, I. / Field, M. / Shoeman, R.L. / Bourgeois, D. / Colletier, J.P. / Schlichting, I. / Weik, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.7 KB | Display | ![]() |
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PDB format | ![]() | 87.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435.2 KB | Display | ![]() |
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Full document | ![]() | 440.8 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5o89C ![]() 5o8bC ![]() 5o8cC ![]() 5dtyS S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
Experimental dataset #2 | Data reference: ![]() |
Experimental dataset #3 | Data reference: ![]() |
Experimental dataset #4 | Data reference: ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28099.686 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: HIS A -8 EXPRESSION TAG HIS A -7 EXPRESSION TAG HIS A -6 EXPRESSION TAG HIS A -5 EXPRESSION TAG HIS A -4 EXPRESSION TAG HIS A -3 EXPRESSION TAG THR A -2 EXPRESSION TAG ASP A -1 EXPRESSION ...Details: HIS A -8 EXPRESSION TAG HIS A -7 EXPRESSION TAG HIS A -6 EXPRESSION TAG HIS A -5 EXPRESSION TAG HIS A -4 EXPRESSION TAG HIS A -3 EXPRESSION TAG THR A -2 EXPRESSION TAG ASP A -1 EXPRESSION TAG PRO A 0 EXPRESSION TAG MET A 1 EXPRESSION TAG VAL A 2 MET 1 ENGINEERED MUTATION LEU A 65 PHE 64 ENGINEERED MUTATION PIA A 68 SER 65 CHROMOPHORE PIA A 68 TYR 66 CHROMOPHORE PIA A 68 GLY 67 CHROMOPHORE LEU A 70 GLN 69 ENGINEERED MUTATION SER A 164 VAL 163 ENGINEERED MUTATION LYS A 207 ALA 206 ENGINEERED MUTATION LEU A 232 HIS 231 ENGINEERED MUTATION Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.51 % |
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Crystal grow | Temperature: 293 K / Method: batch mode / pH: 8 / Details: 2 M ammonium sulphate, 20 mM NaCl, 120 mM HEPES |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: Y |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: May 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→47.021 Å / Num. obs: 25880 / % possible obs: 99.8 % / Redundancy: 665 % / Net I/σ(I): 11.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DTY Resolution: 1.7→17.251 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.33
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→17.251 Å
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Refine LS restraints |
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