+Open data
-Basic information
Entry | Database: PDB / ID: 6jxf | |||||||||
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Title | Photoswitchable fluorescent protein Gamillus, off-state (pH7.0) | |||||||||
Components | Green fluorescent protein | |||||||||
Keywords | FLUORESCENT PROTEIN / acid-tolerant / photoswitchable / cis-chromophore | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Olindias (invertebrata) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Nakashima, R. / Sakurai, K. / shinoda, H. / Matsuda, T. / Nagai, T. | |||||||||
Citation | Journal: Cell Chem Biol / Year: 2019 Title: Acid-Tolerant Reversibly Switchable Green Fluorescent Protein for Super-resolution Imaging under Acidic Conditions. Authors: Shinoda, H. / Lu, K. / Nakashima, R. / Wazawa, T. / Noguchi, K. / Matsuda, T. / Nagai, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jxf.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jxf.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 6jxf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/6jxf ftp://data.pdbj.org/pub/pdb/validation_reports/jx/6jxf | HTTPS FTP |
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-Related structure data
Related structure data | 6j1aC 6j1bC 6j1cC 5y00S C: citing same article (ref.) S: Starting model for refinement |
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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: 30410.236 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Olindias (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2Z5X7U3*PLUS | ||
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#2: Chemical | ChemComp-PO4 / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 5.79 Å3/Da / Density % sol: 78.77 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Ammonium phosphate, sodium citrate, sodium chloride, HEPES, pH5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Nov 18, 2016 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→46.682 Å / Num. obs: 64910 / % possible obs: 99.7 % / Redundancy: 7.408 % / Biso Wilson estimate: 32.623 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.069 / Χ2: 1.039 / Net I/σ(I): 17.34 / Num. measured all: 480868 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5Y00 Resolution: 1.8→46.68 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.223 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.056 / 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: 96.23 Å2 / Biso mean: 29.584 Å2 / Biso min: 17.51 Å2
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Refinement step | Cycle: final / Resolution: 1.8→46.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.798→1.845 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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