+Open data
-Basic information
Entry | Database: PDB / ID: 3hjk | ||||||
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Title | 2.0 Angstrom Structure of the Ile74Val Variant of Vivid (VVD). | ||||||
Components | Vivid PAS protein VVD | ||||||
Keywords | SIGNALING PROTEIN / Photoreceptor / Circadian Clock / FAD / LOV / PAS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neurospora crassa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Zoltowski, B.D. / Vaccaro, B.J. / Crane, B.R. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2009 Title: Mechanism-based tuning of a LOV domain photoreceptor. Authors: Zoltowski, B.D. / Vaccaro, B. / Crane, B.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hjk.cif.gz | 81.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hjk.ent.gz | 60.4 KB | Display | PDB format |
PDBx/mmJSON format | 3hjk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/3hjk ftp://data.pdbj.org/pub/pdb/validation_reports/hj/3hjk | HTTPS FTP |
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-Related structure data
Related structure data | 3hjiC 2pd7S 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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2 |
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Unit cell |
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Details | The protein in monomeric, however following photo-excitation the protein dimerizes. The biological dimer structure is currently unknown. |
-Components
#1: Protein | Mass: 17498.977 Da / Num. of mol.: 2 / Mutation: I74V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Gene: G17A4.050, Vivid, vvd / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9C3Y6 #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: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Protein at 3.6 mg/ml dissolved in Buffer containing 5 mM DTT, 100 mM NaCl, 50 mM HEPES pH 8.0 and 10% glycerol is combined with an equal volume of 28% PEG 4k, 100 mM ammonium acetate, 100 mM ...Details: Protein at 3.6 mg/ml dissolved in Buffer containing 5 mM DTT, 100 mM NaCl, 50 mM HEPES pH 8.0 and 10% glycerol is combined with an equal volume of 28% PEG 4k, 100 mM ammonium acetate, 100 mM trisodium citrate pH 5.6., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 80 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2008 |
Radiation | Monochromator: Double-bounce downward, offset 25.4 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→35.66 Å / Num. all: 21712 / Num. obs: 21712 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 4.5 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 29 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1903 / % possible all: 93.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2pd7 Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 100.24 Å2 / Biso mean: 33.546 Å2 / Biso min: 10.37 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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