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Yorodumi- PDB-5o7y: Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5o7y | ||||||
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Title | Thebaine 6-O-demethylase (T6ODM) from Papaver somniferum in complex with succinate | ||||||
Components | Thebaine 6-O-demethylase | ||||||
Keywords | OXIDOREDUCTASE / 2-oxoglutarate dependent dioxygenase / morphine biosynthesis / oripavine / thebaine | ||||||
Function / homology | Function and homology information thebaine 6-O-demethylase / thebaine 6-O-demethylase activity / oripavine 6-O-demethylase activity / morphine biosynthetic process / methyltransferase activity / methylation / metal ion binding Similarity search - Function | ||||||
Biological species | Papaver somniferum (opium poppy) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.97 Å | ||||||
Authors | Kluza, A. / Niedzialkowska, E. / Kurpiewska, K. / Porebski, P.J. / Borowski, T. | ||||||
Funding support | Poland, 1items
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Citation | Journal: J. Struct. Biol. / Year: 2018 Title: Crystal structure of thebaine 6-O-demethylase from the morphine biosynthesis pathway. Authors: Kluza, A. / Niedzialkowska, E. / Kurpiewska, K. / Wojdyla, Z. / Quesne, M. / Kot, E. / Porebski, P.J. / Borowski, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5o7y.cif.gz | 98.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5o7y.ent.gz | 72.4 KB | Display | PDB format |
PDBx/mmJSON format | 5o7y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o7/5o7y ftp://data.pdbj.org/pub/pdb/validation_reports/o7/5o7y | HTTPS FTP |
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-Related structure data
Related structure data | 5o9wC 4xaeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.18430/m35o7y / Data set type: diffraction image 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: 40936.867 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Papaver somniferum (opium poppy) / Gene: T6ODM, DIOX1 / Plasmid: pMCSG19 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Magic / References: UniProt: D4N500, thebaine 6-O-demethylase |
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-Non-polymers , 5 types, 356 molecules
#2: Chemical | ChemComp-NI / | ||||
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#3: Chemical | ChemComp-SIN / | ||||
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 125 mM sodium succinate, 22% PEG 3350. Concentration of protein 37.5 mg/ml. |
-Data collection
Diffraction | Mean temperature: 130 K |
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Diffraction source | Source: SEALED TUBE / Type: Agilent SuperNova / Wavelength: 1.54 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→41.51 Å / Num. obs: 28189 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 15.8 % / Biso Wilson estimate: 25.4 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 17.71 |
Reflection shell | Resolution: 1.97→2 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 2.271 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4XAE Resolution: 1.97→41.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.396 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.145 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.244 Å2
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Refinement step | Cycle: 1 / Resolution: 1.97→41.51 Å
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Refine LS restraints |
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