+Open data
-Basic information
Entry | Database: PDB / ID: 5dtz | ||||||
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Title | Crystal structure of rsFolder 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: 1.5 Å | ||||||
Authors | El Khatib, M. / Colletier, J.P. / Adam, V. | ||||||
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 | 5dtz.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5dtz.ent.gz | 174 KB | Display | PDB format |
PDBx/mmJSON format | 5dtz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5dtz_validation.pdf.gz | 488.3 KB | Display | wwPDB validaton report |
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Full document | 5dtz_full_validation.pdf.gz | 501 KB | Display | |
Data in XML | 5dtz_validation.xml.gz | 47.4 KB | Display | |
Data in CIF | 5dtz_validation.cif.gz | 69.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/5dtz ftp://data.pdbj.org/pub/pdb/validation_reports/dt/5dtz | HTTPS FTP |
-Related structure data
Related structure data | 5dtxC 5dtyC 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29374.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aequorea victoria (jellyfish) / Gene: GFP / Plasmid: plasmid / Details (production host): pET15-b / Production host: Escherichia coli (E. coli) / References: UniProt: P42212 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.09 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris, 20% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→95.97 Å / Num. obs: 144849 / % possible obs: 97.12 % / Redundancy: 4 % / Rsym value: 0.078 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.1 / % possible all: 81.62 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2B3P Resolution: 1.5→95.97 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.804 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 24.652 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→95.97 Å
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Refine LS restraints |
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