+Open data
-Basic information
Entry | Database: PDB / ID: 5f1e | ||||||
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Title | Apo protein of Sandercyanin | ||||||
Components | Sandercyanin Fluorescent Protein | ||||||
Keywords | FLUORESCENT PROTEIN / Sandercyanin / red-fluorescent protein / lipocalin / biliverdin / photo-stability | ||||||
Function / homology | Function and homology information pigment binding / response to reactive oxygen species / lipid metabolic process / cytoplasm Similarity search - Function | ||||||
Biological species | Sander vitreus (walleye) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Ghosh, S. / Ramaswamy, S. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2016 Title: Blue protein with red fluorescence Authors: Ghosh, S. / Yu, C.L. / Ferraro, D.J. / Sudha, S. / Pal, S.K. / Schaefer, W.F. / Gibson, D.T. / Ramaswamy, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f1e.cif.gz | 78.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f1e.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 5f1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5f1e_validation.pdf.gz | 436.8 KB | Display | wwPDB validaton report |
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Full document | 5f1e_full_validation.pdf.gz | 437.2 KB | Display | |
Data in XML | 5f1e_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 5f1e_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/5f1e ftp://data.pdbj.org/pub/pdb/validation_reports/f1/5f1e | HTTPS FTP |
-Related structure data
Related structure data | 5ez2C 5f6zSC 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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-Components
#1: Protein | Mass: 20159.748 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sander vitreus (walleye) / Tissue: Mucus / Cell line: Mucosa / Plasmid: pET21a Details (production host): Ampicillin resistant plasmid, gene is cloned between NdeI and HindIII Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1D5B367*PLUS #2: 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: 4.12 Å3/Da / Density % sol: 70.2 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M HEPES, 10% PEG 8000, 8% v/v Ethylene glycol / PH range: 7.4-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.987 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 24, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.987 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→53.4 Å / Num. obs: 17824 / % possible obs: 99.98 % / Redundancy: 36.7 % / Rsym value: 0.129 / Net I/σ(I): 31.48 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F6Z Resolution: 2.7→53.4 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.09 / 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: 2.7→53.4 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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