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Yorodumi- PDB-3ngc: Complex of 6-hydroxy-L-nicotine oxidase with intermediate methylm... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ngc | ||||||
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Title | Complex of 6-hydroxy-L-nicotine oxidase with intermediate methylmyosmine product formed during catalytic turnover | ||||||
Components | 6-hydroxy-L-nicotine oxidase | ||||||
Keywords | OXIDOREDUCTASE / ENANTHIOMERIC SUBSTRATE-INHIBITOR / FLAVOENZYMES / NICOTINE DEGRADATION | ||||||
Function / homology | Function and homology information (S)-6-hydroxynicotine oxidase / (S)-6-hydroxynicotine oxidase activity / nicotine catabolic process / alkaloid metabolic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | Arthrobacter nicotinovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Kachalova, G.S. / Bartunik, H.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Crystal structure analysis of free and substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans. Authors: Kachalova, G.S. / Bourenkov, G.P. / Mengesdorf, T. / Schenk, S. / Maun, H.R. / Burghammer, M. / Riekel, C. / Decker, K. / Bartunik, H.D. #1: Journal: J.Mol.Biol. / Year: 2010 Title: Crystal structure analysis of free and substrate-bound 6-hydroxy-L-nicotine from Arthrobacter nicotinovorans Authors: Kachalova, G.S. / Bourenkov, G.P. / Mengesdorf, T. / Schenk, S. / Maun, H.R. / Burghammer, M. / Riekel, C. / Decker, K. / Bartunik, H.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ngc.cif.gz | 113.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ngc.ent.gz | 85 KB | Display | PDB format |
PDBx/mmJSON format | 3ngc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/3ngc ftp://data.pdbj.org/pub/pdb/validation_reports/ng/3ngc | HTTPS FTP |
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-Related structure data
Related structure data | 3k7mC 3k7qC 3k7tC 3nh3C 3nhoC 3nk0C 3nk1C 3nk2C 3nn0C 3nn6C 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules X
#1: Protein | Mass: 47214.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter nicotinovorans (bacteria) / Strain: gram-positive soil bacterium / Gene: 6-HLNO / Plasmid: pTrc99A / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: Q93NH4, (S)-6-hydroxynicotine oxidase |
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-Non-polymers , 5 types, 462 molecules
#2: Chemical | ChemComp-HNL / |
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#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-GP7 / ( |
#5: Chemical | ChemComp-HNH / |
#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: 3.81 Å3/Da / Density % sol: 67.68 % |
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Crystal grow | Temperature: 293 K / pH: 7.5 Details: 20mM Sodium phosphate; 4M sodium formiate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 17, 2003 / Details: MIRROR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→20 Å / Num. obs: 34405 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 34.45 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.25→2.33 Å / Redundancy: 3 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 2 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→12.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.933 / SU B: 4.542 / SU ML: 0.116 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.25→12.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.25→2.31 Å / Total num. of bins used: 20
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