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Yorodumi- PDB-6i21: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i21 | ||||||
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Title | Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism | ||||||
Components | Aureochrome1-like protein | ||||||
Keywords | TRANSCRIPTION / LOV Domain / FMN / Dark grown / fluorescence / light sensing / transcription factor PAS domain / Ochronomas danica | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / nucleotide binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | Ochromonas danica (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 6i21.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6i21.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 6i21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6i21_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6i21_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6i21_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 6i21_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i2/6i21 ftp://data.pdbj.org/pub/pdb/validation_reports/i2/6i21 | HTTPS FTP |
-Related structure data
Related structure data | 6i20C 6i22C 6i23C 6i24C 6i25C 5a8bS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 15012.846 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, 143 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-CL / | #4: Chemical | #5: Chemical | #6: Chemical | #7: 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 grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 10-25% PEG 2K or 3K, 100 mM Na Acetate or Na Citrate, pH 4.5 - 4.9 Protein conc 10 mg/ml |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→67.48 Å / Num. obs: 36515 / % possible obs: 100 % / Redundancy: 20.7 % / Biso Wilson estimate: 22.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.074 / Net I/av σ(I): 18.2 / Net I/σ(I): 18.2 |
Reflection shell | Resolution: 1.5→1.54 Å / Redundancy: 21.3 % / Rmerge(I) obs: 2.595 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2637 / CC1/2: 0.644 / Rrim(I) all: 2.725 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5A8B Resolution: 1.5→67.48 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.97 / SU B: 3.686 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.062 / 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: 26.378 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→67.48 Å
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Refine LS restraints |
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