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- PDB-6i24: Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism -
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Open data
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Basic information
Entry | Database: PDB / ID: 6i24 | ||||||
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Title | Flavin Analogue Sheds Light on Light-Oxygen-Voltage Domain Mechanism | ||||||
![]() | Aureochrome1-like protein | ||||||
![]() | TRANSCRIPTION / LOV Domain / FMN / Dark grown / fluorescence / light sensing / transcription factor PAS domain / Ochronomas danica | ||||||
Function / homology | ![]() DNA-binding transcription factor activity / nucleotide binding / nucleus / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rizkallah, P.J. / Kalvaitis, M.E. / Allemann, R.K. / Mart, R.J. / Johnson, L.A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81.1 KB | Display | ![]() |
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PDB format | ![]() | 58.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6i20C ![]() 6i21C ![]() 6i22C ![]() 6i23C ![]() 6i25C ![]() 5a8bS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 154 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/5DD.gif)
![](data/chem/img/9O9.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/5DD.gif)
![](data/chem/img/9O9.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / | ||||||||
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#3: Chemical | ChemComp-CL / | ||||||||
#4: Chemical | ChemComp-MG / | ||||||||
#5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / | #7: Chemical | ChemComp-5DD / [( | #8: Chemical | ChemComp-9O9 / | #9: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 10 - 25 % PEG 2K or 3K 0.1 M Na Acetate or Citrate 0.1 M NH4Cl PH range: 4.5 - 4.9 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 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: 1.43→67.49 Å / Num. obs: 41996 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 17 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.089 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.43→1.47 Å / Redundancy: 19.7 % / Rmerge(I) obs: 2.114 / Num. unique obs: 3051 / CC1/2: 0.741 / Rrim(I) all: 2.229 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5A8B Resolution: 1.43→67.49 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.422 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.267 Å2
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Refinement step | Cycle: 1 / Resolution: 1.43→67.49 Å
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Refine LS restraints |
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