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Yorodumi- PDB-3d72: 1.65 Angstrom crystal structure of the Cys71Val variant in the fu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3d72 | ||||||
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Title | 1.65 Angstrom crystal structure of the Cys71Val variant in the fungal photoreceptor VVD | ||||||
Components | Vivid PAS protein VVD | ||||||
Keywords | SIGNALING PROTEIN / Circadian / photoreceptor / blue-light / LOV / PAS / VVD | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neurospora crassa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Zoltowski, B.D. / Crane, B.R. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Light activation of the LOV protein vivid generates a rapidly exchanging dimer. Authors: Zoltowski, B.D. / 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 | 3d72.cif.gz | 86 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d72.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 3d72.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d7/3d72 ftp://data.pdbj.org/pub/pdb/validation_reports/d7/3d72 | HTTPS FTP |
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-Related structure data
Related structure data | 2pd7S 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: 16996.496 Da / Num. of mol.: 2 / Fragment: Fungal Photoreceptor VVD / Mutation: c71v Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Gene: vvd, G17A4.050 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q9C3Y6, UniProt: Q1K5Y8*PLUS #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: 2.47 Å3/Da / Density % sol: 50.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 26% PEG 4000, 100 mM triSodium Citrate pH 5.6, 100 mM Sodium Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9179 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 27, 2007 |
Radiation | Monochromator: Horizontal bent Si(111), asymmetrically cut with water cooled Cu Block Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→50 Å / Num. all: 39657 / Num. obs: 39115 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 16.93 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 37.95 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 6.9 / Num. unique all: 3682 / % possible all: 94.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PD7 Resolution: 1.65→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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