+Open data
-Basic information
Entry | Database: PDB / ID: 5dtx | ||||||
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Title | Crystal structure of rsEGFP2 in the fluorescent on-state | ||||||
Components | Green fluorescent protein | ||||||
Keywords | FLUORESCENT PROTEIN / GFP / reversibly switchable / cis 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 / MOLECULAR REPLACEMENT / Resolution: 1.45 Å | ||||||
Authors | Adam, V. / 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 | 5dtx.cif.gz | 73.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dtx.ent.gz | 52.1 KB | Display | PDB format |
PDBx/mmJSON format | 5dtx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dtx_validation.pdf.gz | 425.8 KB | Display | wwPDB validaton report |
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Full document | 5dtx_full_validation.pdf.gz | 428 KB | Display | |
Data in XML | 5dtx_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 5dtx_validation.cif.gz | 23.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/5dtx ftp://data.pdbj.org/pub/pdb/validation_reports/dt/5dtx | HTTPS FTP |
-Related structure data
Related structure data | 5dtyC 5dtzC 5du0C 2b3pS S: Starting model for refinement C: citing same article (ref.) |
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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
#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 / Plasmid: pQE-31 / 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: 39.16 % |
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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 | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→47.04 Å / Num. obs: 40827 / % possible obs: 99.35 % / Redundancy: 4.3 % / Rsym value: 0.052 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.3 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 1.45→47.039 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.33 / 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: 1.45→47.039 Å
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Refine LS restraints |
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LS refinement shell |
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