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Yorodumi- PDB-6ttm: Hyoscyamine 6-hydroxylase in complex with N-oxalylglycine and hyo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ttm | ||||||
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Title | Hyoscyamine 6-hydroxylase in complex with N-oxalylglycine and hyoscyamine | ||||||
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: 1.91 Å | ||||||
Authors | Kluza, A. / Kurpiewska, K. / Mrugala, B. / Porebski, P.J. / Niedzialkowska, E. / Minor, W. / 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 | 6ttm.cif.gz | 148.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ttm.ent.gz | 111.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ttm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ttm_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ttm_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ttm_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 6ttm_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tt/6ttm ftp://data.pdbj.org/pub/pdb/validation_reports/tt/6ttm | HTTPS FTP |
-Related structure data
Related structure data | 6ttnC 6ttoC 1gp6S 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: 39863.465 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: SNA - purification tag fragment remained after TEV protease cleavage. N-terminal, C-terminal 3-residues and two loops are disordered. 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 , 8 types, 214 molecules
#2: Chemical | ChemComp-PEG / | ||||||
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#3: Chemical | ChemComp-HYO / [( | ||||||
#4: Chemical | ChemComp-NI / | ||||||
#5: Chemical | ChemComp-OGA / | ||||||
#6: Chemical | #7: Chemical | ChemComp-SR / | #8: Chemical | #9: 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: 2.39 Å3/Da / Density % sol: 48.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein sample: 20 mg/ml H6H in water, 100 mM N-oxalylglycine, 10 mM hyoscyamine. Mother liquor: 100 mM strontium chloride, 180 mM sodium formate, 21% PEG 3350. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. obs: 29418 / % possible obs: 96.9 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.043 / Rsym value: 0.038 / Net I/σ(I): 25.1 |
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 1.971 / Num. unique obs: 1324 / CC1/2: 0.897 / Rrim(I) all: 0.392 / Rsym value: 0.344 / % possible all: 90.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1GP6 Resolution: 1.91→49.24 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 125.55 Å2 / Biso mean: 46.3396 Å2 / Biso min: 20.27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.91→49.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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