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Open data
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Basic information
Entry | Database: PDB / ID: 3nk1 | ||||||
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Title | Complex of 6-hydroxy-L-nicotine oxidase with serotonin | ||||||
![]() | 6-hydroxy-L-nicotine oxidase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. #1: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
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PDB format | ![]() | 85.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3k7mSC ![]() 3k7qC ![]() 3k7tC ![]() 3ngcC ![]() 3nh3C ![]() 3nhoC ![]() 3nk0C ![]() 3nk2C ![]() 3nn0C ![]() 3nn6C C: citing same article ( S: Starting model for refinement |
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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-SRO / ![]() |
#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: 3.92 Å3/Da / Density % sol: 68.6 % |
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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 165 mm / Detector: CCD / Date: May 10, 2009 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→20 Å / Num. all: 38995 / Num. obs: 38117 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Biso Wilson estimate: 37.33 Å2 / Rmerge(I) obs: 0.115 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1918 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB code 3K7M Resolution: 2.2→14.4 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.048 / SU ML: 0.104 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.162 / 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: 35.228 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→14.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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