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Yorodumi- PDB-5nmw: Crystal Structure of the pyrrolizidine alkaloid N-oxygenase from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nmw | ||||||
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Title | Crystal Structure of the pyrrolizidine alkaloid N-oxygenase from Zonocerus variegatus in complex with FAD | ||||||
Components | Flavin-containing monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / pyrrolizidine alkaloid N-oxygenase / flavin-containing monooxygenase / rossmann fold / FAD / two dinucleotide binding domain flavoprotein / senecionine | ||||||
Function / homology | Function and homology information N,N-dimethylaniline monooxygenase activity / Oxidoreductases / flavin adenine dinucleotide binding / NADP binding Similarity search - Function | ||||||
Biological species | Zonocerus variegatus (insect) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Scheidig, A. / Kubitza, C. / Faust, A. / Ober, D. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2018 Title: Crystal structure of pyrrolizidine alkaloid N-oxygenase from the grasshopper Zonocerus variegatus. Authors: Kubitza, C. / Faust, A. / Gutt, M. / Gath, L. / Ober, D. / Scheidig, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nmw.cif.gz | 367.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nmw.ent.gz | 296.3 KB | Display | PDB format |
PDBx/mmJSON format | 5nmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/5nmw ftp://data.pdbj.org/pub/pdb/validation_reports/nm/5nmw | HTTPS FTP |
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-Related structure data
Related structure data | 5nmxC 2xveS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 49299.051 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zonocerus variegatus (insect) / Gene: pno / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L0N8S9, Oxidoreductases #2: Chemical | ChemComp-FAD / #3: Chemical | #4: Water | ChemComp-HOH / | |
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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: 2.2 Å3/Da / Density % sol: 43.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: TRIS-HCl, MgCl2, PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→76.5 Å / Num. obs: 119135 / % possible obs: 90.2 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.89→1.92 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 2 / % possible all: 62.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2xve Resolution: 1.89→76.46 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.941 / SU B: 0.004 / SU ML: 0 / SU R Cruickshank DPI: 0.1373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.157 / Details: U VALUES : REFINED INDIVIDUALLY
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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 max: 75.32 Å2 / Biso mean: 31.3818 Å2 / Biso min: 12.08 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→76.46 Å
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LS refinement shell | Resolution: 1.89→1.939 Å / Total num. of bins used: 20
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