+Open data
-Basic information
Entry | Database: PDB / ID: 4i3c | ||||||
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Title | Crystal structure of fluorescent protein UnaG N57Q mutant | ||||||
Components | Bilirubin-inducible fluorescent protein UnaG | ||||||
Keywords | FLUORESCENT PROTEIN / Bilirubin binding protein / Lipocalin / Beta barrel / Cytosol | ||||||
Function / homology | Function and homology information fatty acid transport / bioluminescence / fatty acid binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Anguilla japonica (Japanese eel) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.001 Å | ||||||
Authors | Kumagai, A. / Ando, R. / Miyatake, H. / Miyawaki, A. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2013 Title: A bilirubin-inducible fluorescent protein from eel muscle Authors: Kumagai, A. / Ando, R. / Miyatake, H. / Greimel, P. / Kobayashi, T. / Hirabayashi, Y. / Shimogori, T. / Miyawaki, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i3c.cif.gz | 142 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i3c.ent.gz | 110.1 KB | Display | PDB format |
PDBx/mmJSON format | 4i3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/4i3c ftp://data.pdbj.org/pub/pdb/validation_reports/i3/4i3c | HTTPS FTP |
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-Related structure data
Related structure data | 4i3bSC 4i3dC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15617.797 Da / Num. of mol.: 2 / Mutation: N57Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anguilla japonica (Japanese eel) / Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0DM59 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.95 Å3/Da / Density % sol: 36.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1M Tris, 30%w/v Polyethylene glycol monomethyl ether 2000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 11, 2012 |
Radiation | Monochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 15849 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 12.46 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 9.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.8 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I3B Resolution: 2.001→35.304 Å / Cross valid method: THROUGHOUT / σ(F): 1.97 / σ(I): 0 / Phase error: 17.57 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.001→35.304 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6
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