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- PDB-3k7t: Crystal structure of apo-form 6-hydroxy-L-nicotine oxidase, cryst... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3k7t | ||||||
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Title | Crystal structure of apo-form 6-hydroxy-L-nicotine oxidase, crystal form P3121 | ||||||
![]() | 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 | ![]() | 180.3 KB | Display | ![]() |
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PDB format | ![]() | 143.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 35.2 KB | Display | |
Data in CIF | ![]() | 45.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3k7mSC ![]() 3k7qC ![]() 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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Unit cell |
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Components
#1: Protein | Mass: 46385.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.7 Å3/Da / Density % sol: 73.84 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Hepes, 1.5M lithium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2002 / Details: mirrors |
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: 2.85→20 Å / Num. all: 41415 / Num. obs: 41084 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 72.9 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 2.85→2.9 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Num. unique all: 2038 / Rsym value: 0.75 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: MOLREP Starting model: PDB ENTRY 3K7M Resolution: 2.85→16.6 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.895 / SU B: 18.93 / SU ML: 0.345 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / ESU R: 0.621 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 72.942 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→16.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.85→2.922 Å / Total num. of bins used: 20
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