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- PDB-3k7q: Crystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k7q | ||||||
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Title | Crystal structure of substrate-bound 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans | ||||||
![]() | 6-hydroxy-L-nicotine oxidase | ||||||
![]() | OXIDOREDUCTASE / ENANTIOMERIC SUBSTRATES / FLAVOENZYMES / NICOTINE DEGRADATION / OXIDASE | ||||||
Function / homology | ![]() (S)-6-hydroxynicotine oxidase / (S)-6-hydroxynicotine oxidase activity / nicotine catabolic process / alkaloid metabolic process / nucleotide binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Bourenkov, G.P. / Kachalova, G.S. / Bartunik, H.D. | ||||||
![]() | ![]() 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 110.4 KB | Display | ![]() |
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PDB format | ![]() | 82.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 941.3 KB | Display | ![]() |
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Full document | ![]() | 950.7 KB | Display | |
Data in XML | ![]() | 23.1 KB | Display | |
Data in CIF | ![]() | 33.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k7mSC ![]() 3k7tC ![]() 3ngcC ![]() 3nh3C ![]() 3nhoC ![]() 3nk0C ![]() 3nk1C ![]() 3nk2C ![]() 3nn0C ![]() 3nn6C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 47214.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-HNL / |
#3: Chemical | ChemComp-FAD / |
#4: Chemical | ChemComp-GP7 / ( |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.89 Å3/Da / Density % sol: 68.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / 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: ![]() ![]() ![]() |
Detector | Type: MAR CCD 130 mm / Detector: CCD / Date: Nov 18, 2001 / Details: KB-mirror |
Radiation | Monochromator: N2 cooled Si-111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.782 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. all: 47039 / Num. obs: 47039 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 11 % / Biso Wilson estimate: 31.38 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.05→2.1 Å / Redundancy: 11 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3282 / Rsym value: 0.71 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: MOLREP Starting model: PDB ENTRY 3K7M Resolution: 2.05→12.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.397 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.389 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→12.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.102 Å / Total num. of bins used: 20
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