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Yorodumi- PDB-2pd7: 2.0 Angstrom Crystal Structure of the Fungal Blue-Light Photorece... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pd7 | ||||||
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Title | 2.0 Angstrom Crystal Structure of the Fungal Blue-Light Photoreceptor 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: 2 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 | 2pd7.cif.gz | 82.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pd7.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pd7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/2pd7 ftp://data.pdbj.org/pub/pdb/validation_reports/pd/2pd7 | HTTPS FTP |
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-Related structure data
Related structure data | 2pd8C 2pdrC 6cnyC 1g28S 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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-Components
#1: Protein | Mass: 17000.510 Da / Num. of mol.: 2 / Fragment: residues 37-184 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: 2.51 Å3/Da / Density % sol: 51.05 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 30% PEG 5000 MME, 0.1M Ammonium Acetate, 0.1M tri-sodium Citrate, 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: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2005 |
Radiation | Monochromator: Double silicon crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20791 / Num. obs: 20707 / % possible obs: 92.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.72 / Net I/σ(I): 22.56 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.202 / Mean I/σ(I) obs: 4.32 / Num. unique all: 1477 / % possible all: 66.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1g28 Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 44.516 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.083 Å2
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Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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Xplor file |
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