+Open data
-Basic information
Entry | Database: PDB / ID: 5dty | ||||||
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Title | Crystal structure of rsEGFP2 in the non-fluorescent off-state | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / GFP / reversibly switchable / trans chromophore | ||||||
Function / homology | Function and homology information serine-type endopeptidase inhibitor activity / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Aequorea victoria (jellyfish) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Adam, V. / Dos-Santos Martins, A. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Rational design of ultrastable and reversibly photoswitchable fluorescent proteins for super-resolution imaging of the bacterial periplasm. Authors: El Khatib, M. / Martins, A. / Bourgeois, D. / Colletier, J.P. / Adam, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5dty.cif.gz | 69.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dty.ent.gz | 53.7 KB | Display | PDB format |
PDBx/mmJSON format | 5dty.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dty_validation.pdf.gz | 434.3 KB | Display | wwPDB validaton report |
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Full document | 5dty_full_validation.pdf.gz | 440 KB | Display | |
Data in XML | 5dty_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | 5dty_validation.cif.gz | 24.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/5dty ftp://data.pdbj.org/pub/pdb/validation_reports/dt/5dty | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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 Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 0.1 M HEPES, 1.7 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→46.91 Å / Num. obs: 36769 / % possible obs: 98.13 % / Redundancy: 4.6 % / Rsym value: 0.075 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 1.2 / % possible all: 91.59 |
-Processing
Software |
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Refinement | Resolution: 1.5→46.91 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.24 / Phase error: 22.44 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→46.91 Å
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Refine LS restraints |
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LS refinement shell |
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