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Yorodumi- PDB-6i20: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i20 | |||||||||
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Title | Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism | |||||||||
Components | (Aureochrome1-like ...) x 2 | |||||||||
Keywords | TRANSCRIPTION / LOV Domain / FMN / Dark grown / fluorescence / light sensing / transcription factor PAS domain / Ochronomas danica | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Ochromonas danica (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.37 Å | |||||||||
Authors | Rizkallah, P.J. / Kalvaitis, M.E. / Allemann, R.K. / Mart, R.J. / Johnson, L.A. | |||||||||
Citation | Journal: Biochemistry / Year: 2019 Title: A Noncanonical Chromophore Reveals Structural Rearrangements of the Light-Oxygen-Voltage Domain upon Photoactivation. Authors: Kalvaitis, M.E. / Johnson, L.A. / Mart, R.J. / Rizkallah, P. / Allemann, R.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6i20.cif.gz | 259.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i20.ent.gz | 216.2 KB | Display | PDB format |
PDBx/mmJSON format | 6i20.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/6i20 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/6i20 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Aureochrome1-like ... , 2 types, 4 molecules ACDB
#1: Protein | Mass: 14883.666 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochromonas danica (eukaryote) / Gene: OdAUREO1 / Production host: Escherichia coli (E. coli) / References: UniProt: C5NSW6 #2: Protein | | Mass: 14898.744 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Ochromonas danica (eukaryote) / Gene: OdAUREO1 / Production host: Escherichia coli (E. coli) / References: UniProt: C5NSW6 |
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-Non-polymers , 6 types, 670 molecules
#3: Chemical | ChemComp-FMN / #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ACT / | #6: Chemical | ChemComp-CL / #7: Chemical | ChemComp-MES / | #8: 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: 2.99 Å3/Da / Density % sol: 58.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.1 M Na Acetate, 0.1 NH4Cl, 15-20 % PEG 2000 pH 4.5-4.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96858 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96858 Å / Relative weight: 1 |
Reflection | Resolution: 1.37→55.54 Å / Num. obs: 152478 / % possible obs: 99.9 % / Redundancy: 18.7 % / Biso Wilson estimate: 16.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.112 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.37→1.41 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.278 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 10991 / CC1/2: 0.546 / Rrim(I) all: 1.377 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.37→55.54 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.869 / SU ML: 0.033 / Cross valid method: THROUGHOUT / ESU R: 0.048 / ESU R Free: 0.046 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.941 Å2
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Refinement step | Cycle: 1 / Resolution: 1.37→55.54 Å
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Refine LS restraints |
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