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- PDB-8cvf: Structure of L289F Hyoscyamine 6-beta Hydroxylase in complex with... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8cvf | ||||||
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Title | Structure of L289F Hyoscyamine 6-beta Hydroxylase in complex with vanadyl, succinate, and hyoscyamine | ||||||
![]() | Hyoscyamine 6-beta-hydroxylase | ||||||
![]() | OXIDOREDUCTASE / oxacyclase / scopolamine / epoxide | ||||||
Function / homology | ![]() hyoscyamine (6S)-dioxygenase / hyoscyamine (6S)-dioxygenase activity / coumarin biosynthetic process / response to molecule of fungal origin / L-ascorbic acid binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wenger, E.W. / Boal, A.K. / Bollinger, J.M. / Krebs, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the L289F H6H ferryl-mimicking complex Authors: Wenger, E.S. / Boal, A.K. / Bollinger, J.M. / Krebs, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96 KB | Display | ![]() |
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PDB format | ![]() | 65.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6ttmS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42666.984 Da / Num. of mol.: 1 / Mutation: L289F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 8 types, 377 molecules ![](data/chem/img/EDO.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HYO.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/V.gif)
![](data/chem/img/O.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HYO.gif)
![](data/chem/img/SIN.gif)
![](data/chem/img/V.gif)
![](data/chem/img/O.gif)
![](data/chem/img/SR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-FMT / #4: Chemical | ChemComp-HYO / [( | #5: Chemical | ChemComp-SIN / | #6: Chemical | ChemComp-V / | #7: Chemical | ChemComp-O / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.07 % / Description: Bar |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, sodium formate, strontium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 16, 2020 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03317 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. obs: 52983 / % possible obs: 97 % / Redundancy: 5.6 % / CC1/2: 0.994 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.053 / Net I/σ(I): 26.4 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 2524 / CC1/2: 0.839 / Rpim(I) all: 0.278 / % possible all: 92.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TTM Resolution: 1.532→43.557 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.238 / SU ML: 0.046 / Cross valid method: FREE R-VALUE / ESU R: 0.079 / ESU R Free: 0.077 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.504 Å2
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Refinement step | Cycle: LAST / Resolution: 1.532→43.557 Å
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Refine LS restraints |
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LS refinement shell |
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