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Yorodumi- PDB-8cvd: Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cvd | ||||||
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Title | Structure of Hyoscyamine 6-beta Hydroxylase in complex with iron, succinate, and scopolamine | ||||||
Components | Hyoscyamine 6-beta-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / oxacyclase / scopolamine / epoxide | ||||||
Function / homology | Function and homology information 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 | Atropa belladonna (belladonna) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.717 Å | ||||||
Authors | Wenger, E.W. / Boal, A.K. / Bollinger, J.M. / Krebs, C. | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Structure of the H6H cyclization product complex Authors: Wenger, E.S. / Boal, A.K. / Bollinger, J.M. / Krebs, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cvd.cif.gz | 91.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cvd.ent.gz | 62.4 KB | Display | PDB format |
PDBx/mmJSON format | 8cvd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cv/8cvd ftp://data.pdbj.org/pub/pdb/validation_reports/cv/8cvd | 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 & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42632.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Atropa belladonna (belladonna) / Gene: AbH6H, h6h / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XJ43, hyoscyamine (6S)-dioxygenase |
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-Non-polymers , 7 types, 201 molecules
#2: Chemical | ChemComp-FE2 / | ||||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-FMT / #5: Chemical | ChemComp-OW0 / ( | #6: Chemical | ChemComp-SIN / | #7: Chemical | #8: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 2.15 Å3/Da / Density % sol: 42.88 % / 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: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 11, 2021 |
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: 1.717→50 Å / Num. obs: 37388 / % possible obs: 98.1 % / Redundancy: 6.1 % / CC1/2: 0.988 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.054 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 1.717→1.75 Å / Redundancy: 4 % / Rmerge(I) obs: 1.098 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1909 / CC1/2: 0.536 / Rpim(I) all: 0.599 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TTM Resolution: 1.717→43.599 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.042 / SU ML: 0.066 / Cross valid method: FREE R-VALUE / ESU R: 0.11 / ESU R Free: 0.099 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: 20.502 Å2
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Refinement step | Cycle: LAST / Resolution: 1.717→43.599 Å
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Refine LS restraints |
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LS refinement shell |
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