+Open data
-Basic information
Entry | Database: PDB / ID: 4zbl | ||||||||||||
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Title | Phototoxic fluorescent protein mKillerOrange | ||||||||||||
Components | KillerOrange | ||||||||||||
Keywords | FLUORESCENT PROTEIN / Phototoxicity / Beta-barrel / QWG chromophore | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Hydrozoa (hydrozoans) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å | ||||||||||||
Authors | Pletnev, V.Z. / Pletneva, N.V. / Pletnev, S.V. | ||||||||||||
Funding support | Russian Federation, 1items
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Citation | Journal: Plos One / Year: 2015 Title: Crystal Structure of Phototoxic Orange Fluorescent Proteins with a Tryptophan-Based Chromophore. Authors: Pletneva, N.V. / Pletnev, V.Z. / Sarkisyan, K.S. / Gorbachev, D.A. / Egorov, E.S. / Mishin, A.S. / Lukyanov, K.A. / Dauter, Z. / Pletnev, S. #1: Journal: J. Biol. Chem. / Year: 2009 Title: Structural basis for phototoxicity of the genetically encoded photosensitizer KillerRed. Authors: Pletnev, S. / Gurskaya, N.G. / Pletneva, N.V. / Lukyanov, K.A. / Chudakov, D.M. / Martynov, V.I. / Popov, V.O. / Kovalchuk, M.V. / Wlodawer, A. / Dauter, Z. / Pletnev, V. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zbl.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zbl.ent.gz | 48.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zbl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zb/4zbl ftp://data.pdbj.org/pub/pdb/validation_reports/zb/4zbl | HTTPS FTP |
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-Related structure data
Related structure data | 4zfsC 3gb3S 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: 27063.434 Da / Num. of mol.: 1 / Mutation: Y66W Source method: isolated from a genetically manipulated source Details: KillerOrange / Source: (gene. exp.) Hydrozoa (hydrozoans) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q2TCH5 | ||
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#2: Chemical | ChemComp-CIT / | ||
#3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 45.15 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.5 / Details: 0.09M citric acid, pH 3.5, 22.5% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 14, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.57→50 Å / Num. obs: 29879 / % possible obs: 98.1 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.024 / Rrim(I) all: 0.047 / Χ2: 0.93 / Net I/av σ(I): 31.322 / Net I/σ(I): 12.4 / Num. measured all: 115789 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GB3 Resolution: 1.57→27.8 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1748 / WRfactor Rwork: 0.1452 / FOM work R set: 0.9029 / SU R Cruickshank DPI: 0.075 / SU Rfree: 0.0764 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.076 / 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: 62.37 Å2 / Biso mean: 16.076 Å2 / Biso min: 6.71 Å2
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Refinement step | Cycle: final / Resolution: 1.57→27.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.57→1.611 Å / Total num. of bins used: 20
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