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Yorodumi- PDB-6gbv: A fast recovering full-length LOV protein (DsLOV) from the marine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gbv | ||||||
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Title | A fast recovering full-length LOV protein (DsLOV) from the marine phototrophic bacterium Dinoroseobacter shibae (Dark state) - M49T mutant | ||||||
Components | Putative blue-light photoreceptor | ||||||
Keywords | SIGNALING PROTEIN / LIGHT-OXYGEN-VOLTAGE / LOV / PAS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Dinoroseobacter shibae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Granzin, J. / Batra-Safferling, R. / Roellen, K. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Mechanistic Basis of the Fast Dark Recovery of the Short LOV Protein DsLOV from Dinoroseobacter shibae. Authors: Fettweiss, T. / Rollen, K. / Granzin, J. / Reiners, O. / Endres, S. / Drepper, T. / Willbold, D. / Jaeger, K.E. / Batra-Safferling, R. / Krauss, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gbv.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gbv.ent.gz | 46.4 KB | Display | PDB format |
PDBx/mmJSON format | 6gbv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gbv_validation.pdf.gz | 736.8 KB | Display | wwPDB validaton report |
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Full document | 6gbv_full_validation.pdf.gz | 737.2 KB | Display | |
Data in XML | 6gbv_validation.xml.gz | 8 KB | Display | |
Data in CIF | 6gbv_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gb/6gbv ftp://data.pdbj.org/pub/pdb/validation_reports/gb/6gbv | HTTPS FTP |
-Related structure data
Related structure data | 6gayC 6gb3C 6gbaC 4kukS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16830.828 Da / Num. of mol.: 1 / Mutation: M49T Source method: isolated from a genetically manipulated source Details: C-terminal hexa-histidine-tagged fusion proteins (tag sequence: LEHHHHHH) in E. coli BL21(DE3) Source: (gene. exp.) Dinoroseobacter shibae (strain DSM 16493 / NCIMB 14021 / DFL 12) (bacteria) Strain: DSM 16493 / NCIMB 14021 / DFL 12 / Gene: Dshi_2006 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A8LP63 |
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#2: Chemical | ChemComp-FMN / |
#3: Chemical | ChemComp-PO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.31 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES sodium, 0.8 M Sodium phosphate monobasic monohydrate, 0.8 M Potassium phosphate monobasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→45.52 Å / Num. obs: 15724 / % possible obs: 98.4 % / Redundancy: 4.7 % / Biso Wilson estimate: 16.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.072 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.63→1.66 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 760 / CC1/2: 0.699 / Rrim(I) all: 0.794 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4KUK Resolution: 1.63→26.2 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.53
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→26.2 Å
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Refine LS restraints |
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LS refinement shell |
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