+Open data
-Basic information
Entry | Database: PDB / ID: 7amb | |||||||||
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Title | Crystal structure of rsFolder2 in its fluorescent on-state | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | FLUORESCENT PROTEIN / GFP / Reversibly Photoswitchable Fluorescent Protein / Photoconvertible FP | |||||||||
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: 1.63 Å | |||||||||
Authors | Moreno-Chicano, T. / El Khatib, M. / Colletier, J.-P. | |||||||||
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 | 7amb.cif.gz | 236.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7amb.ent.gz | 191.4 KB | Display | PDB format |
PDBx/mmJSON format | 7amb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/7amb ftp://data.pdbj.org/pub/pdb/validation_reports/am/7amb | HTTPS FTP |
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-Related structure data
Related structure data | 7amfC 7o7cC 7o7dC 7o7eC 7o7hC 7o7uC 7o7vC 7o7wC 7o7xC 5dtzS 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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2 |
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3 |
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4 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26724.070 Da / Num. of mol.: 4 Mutation: S30R, Y39N, F64L, S65A, Q69L, Q80R, F99S, N105T, M153T, V163S, I171V, A206K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: P42212 #2: Chemical | ChemComp-GOL / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.21 Å3/Da / Density % sol: 44 % / Description: Large thick plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 20% PEG 3350, 100 mM Tris pH 8.5, 20 mM NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 1, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→47.98 Å / Num. obs: 115478 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 18.43 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.065 / Χ2: 0.98 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 5788 / CC1/2: 0.747 / Rrim(I) all: 0.73 / Χ2: 0.99 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5dtz Resolution: 1.63→47.98 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.295 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 92.55 Å2 / Biso mean: 24.127 Å2 / Biso min: 11.24 Å2
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Refinement step | Cycle: final / Resolution: 1.63→47.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.63→1.672 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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