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Yorodumi- PDB-4kuk: A superfast recovering full-length LOV protein from the marine ph... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kuk | ||||||
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Title | A superfast recovering full-length LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) | ||||||
Components | blue-light photoreceptor | ||||||
Keywords | SIGNALING PROTEIN / PAS domain / light-oxygen-voltage / LOV / FMN Binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dinoroseobacter shibae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Circolone, F. / Granzin, J. / Stadler, A. / Krauss, U. / Drepper, T. / Endres, S. / Knieps-Gruenhagen, E. / Wirtz, A. / Willbold, D. / Batra-Safferling, R. / Jaeger, K.-E. | ||||||
Citation | Journal: BMC Microbiol / Year: 2015 Title: Structure and function of a short LOV protein from the marine phototrophic bacterium Dinoroseobacter shibae. Authors: Endres, S. / Granzin, J. / Circolone, F. / Stadler, A. / Krauss, U. / Drepper, T. / Svensson, V. / Knieps-Grunhagen, E. / Wirtz, A. / Cousin, A. / Tielen, P. / Willbold, D. / Jaeger, K.E. / Batra-Safferling, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kuk.cif.gz | 68.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kuk.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 4kuk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kuk_validation.pdf.gz | 770 KB | Display | wwPDB validaton report |
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Full document | 4kuk_full_validation.pdf.gz | 771.6 KB | Display | |
Data in XML | 4kuk_validation.xml.gz | 8.5 KB | Display | |
Data in CIF | 4kuk_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/4kuk ftp://data.pdbj.org/pub/pdb/validation_reports/ku/4kuk | HTTPS FTP |
-Related structure data
Related structure data | 4kuoC 2v0uS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16873.939 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dinoroseobacter shibae (bacteria) / Strain: DFL 12 / Gene: Dshi_2006 / Plasmid: pBluescript-DsLOV / Production host: Escherichia coli (E. coli) / References: UniProt: A8LP63 |
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#2: Chemical | ChemComp-RBF / |
#3: Chemical | ChemComp-ACY / |
#4: Water | ChemComp-HOH / |
Sequence details | CONFORMATI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.57 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.3 M magnesium chloride, 8% PGA-LM, 0.1 M sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 292.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 26, 2011 |
Radiation | Monochromator: Diamond(001) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→45.4 Å / Num. obs: 19912 / % possible obs: 98.98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 14.08 Å2 / Rsym value: 0.037 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 4.3 / Num. unique all: 884 / % possible all: 89.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2V0U Resolution: 1.5→45.399 Å / SU ML: 0.13 / Isotropic thermal model: ANISOTROPIC/ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 17.18 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→45.399 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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