+Open data
-Basic information
Entry | Database: PDB / ID: 2pd8 | ||||||
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Title | 1.8 Angstrom Crystal Structure of the Cys71Ser mutant of Vivid | ||||||
Components | Vivid PAS protein VVD | ||||||
Keywords | CIRCADIAN CLOCK PROTEIN / LOV Domain / flavin / photoreceptor / circadian clock | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Neurospora crassa (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Zoltowski, B.D. / Crane, B.R. / Bilwes, A.M. | ||||||
Citation | Journal: Science / Year: 2007 Title: Conformational switching in the fungal light sensor Vivid Authors: Zoltowski, B.D. / Schwerdtfeger, C. / Widom, J. / Loros, J.J. / Bilwes, A.M. / Dunlap, J.C. / 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 | 2pd8.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pd8.ent.gz | 60.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/2pd8 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/2pd8 | HTTPS FTP |
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-Related structure data
Related structure data | 2pd7SC 2pdrC 6cnyC 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: 16984.443 Da / Num. of mol.: 2 / Fragment: residues 37-184 / Mutation: C71S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Neurospora crassa (fungus) / Gene: vvd, G17A4.050 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / 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: 2.47 Å3/Da / Density % sol: 50.22 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG 5000 MME, 0.1M tri-sodium citrate, 0.1M Ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 10, 2006 |
Radiation | Monochromator: Double-bounce downward, offset 25.4 mm / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→50 Å / Num. all: 54748 / Num. obs: 54748 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.7 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 21.64 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.81 / Num. unique all: 3636 / % possible all: 60 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PD7 Resolution: 1.8→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 26.453 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.899 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→30 Å
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Refine LS restraints |
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Xplor file |
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