[English] 日本語
![](img/lk-miru.gif)
- PDB-3nn6: Crystal structure of inhibitor-bound in active centre 6-hydroxy-L... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 3nn6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of inhibitor-bound in active centre 6-hydroxy-L-nicotine oxidase from Arthrobacter nicotinovorans | ||||||
![]() | 6-hydroxy-L-nicotine oxidase | ||||||
![]() | OXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / ENANTIOMERIC SUBSTRATE- INHIBITOR / FLAVOENZYMES / NICOTINE DEGRADATION / FAD-binding fold / amino oxidase / FAD binding / ![]() | ||||||
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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 113.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 3k7mSC ![]() 3k7qC ![]() 3k7tC ![]() 3ngcC ![]() 3nh3C ![]() 3nhoC ![]() 3nk0C ![]() 3nk1C ![]() 3nk2C ![]() 3nn0C C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 47214.090 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() |
---|---|
#2: Chemical | ChemComp-HNK / |
#3: Chemical | ChemComp-FB0 / ( |
#4: Chemical | ChemComp-GP7 / ( |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.91 Å3/Da / Density % sol: 68.51 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 17, 2009 / Details: mirror |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.19→20 Å / Num. all: 39391 / Num. obs: 39330 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 34.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.19→2.23 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 3 / Num. unique all: 1909 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: PDB 3K7M Resolution: 2.19→14.4 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / SU B: 4.016 / SU ML: 0.102 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.743 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.19→14.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.19→2.246 Å / Total num. of bins used: 20
|