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Yorodumi- PDB-6tto: N-terminally truncated hyoscyamine 6-hydroxylase (tH6H) in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tto | ||||||
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Title | N-terminally truncated hyoscyamine 6-hydroxylase (tH6H) in complex with 2-oxoglutarate | ||||||
Components | Hyoscyamine 6 beta-hydroxylase | ||||||
Keywords | OXIDOREDUCTASE / jelly-roll / non-heme / 2-oxoglutarate | ||||||
Function / homology | Function and homology information coumarin biosynthetic process / response to molecule of fungal origin / 2-oxoglutarate-dependent dioxygenase activity / L-ascorbic acid binding / metal ion binding Similarity search - Function | ||||||
Biological species | Datura metel (Hindu datura) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å | ||||||
Authors | Kluza, A. / Mrugala, B. / Porebski, P.J. / Kurpiewska, K. / Niedzialkowska, E. / Weiss, M.S. / Borowski, T. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Dalton Trans / Year: 2020 Title: Regioselectivity of hyoscyamine 6 beta-hydroxylase-catalysed hydroxylation as revealed by high-resolution structural information and QM/MM calculations. Authors: Kluza, A. / Wojdyla, Z. / Mrugala, B. / Kurpiewska, K. / Porebski, P.J. / Niedzialkowska, E. / Minor, W. / Weiss, M.S. / Borowski, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tto.cif.gz | 247.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tto.ent.gz | 191.3 KB | Display | PDB format |
PDBx/mmJSON format | 6tto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/6tto ftp://data.pdbj.org/pub/pdb/validation_reports/tt/6tto | HTTPS FTP |
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-Related structure data
Related structure data | 6ttmC 6ttnSC C: citing same article (ref.) S: Starting model for refinement |
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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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36285.492 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SNA - fragment of purification tag remained after TEV protease cleavage Source: (gene. exp.) Datura metel (Hindu datura) / Gene: H6H / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6EZB3 |
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-Non-polymers , 7 types, 416 molecules
#2: Chemical | ChemComp-AKG / | ||||||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-FMT / | #5: Chemical | ChemComp-NI / | #6: Chemical | #7: Chemical | ChemComp-NA / | #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: 2.29 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein sample: 37.5 mg/ml tH6H in water. Mother liquor: 100 mM disodium 2-oxoglutarate, 100 mM strontium chloride, 200 mM sodium formate, 25% PEG 3350. 1.3 uL of protein solution, 1 uL of ...Details: Protein sample: 37.5 mg/ml tH6H in water. Mother liquor: 100 mM disodium 2-oxoglutarate, 100 mM strontium chloride, 200 mM sodium formate, 25% PEG 3350. 1.3 uL of protein solution, 1 uL of mother liquor, 0.3 uL of 100x diluted seeds stock of tH6H:NOG:Hyo crystals. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.31→43.7 Å / Num. obs: 81465 / % possible obs: 99.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.3 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.079 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.31→1.39 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 12961 / CC1/2: 0.578 / Rrim(I) all: 1.366 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6TTN Resolution: 1.31→43.7 Å / SU ML: 0.1589 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.7524
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→43.7 Å
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Refine LS restraints |
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LS refinement shell |
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