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- PDB-4nbb: Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4nbb | ||||||
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Title | Carbazole- and oxygen-bound oxygenase with Ile262 replaced by Val and ferredoxin complex of carbazole 1,9a-dioxygenase | ||||||
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![]() | OXIDOREDUCTASE / Rieske non-heme iron oxygenase / carbazole 1 / 9a-dioxygenase | ||||||
Function / homology | ![]() carbazole catabolic process / ferredoxin hydrogenase activity / dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ashikawa, Y. / Usami, Y. / Inoue, K. / Nojiri, H. | ||||||
![]() | ![]() Title: Structural basis of the divergent oxygenation reactions catalyzed by the rieske nonheme iron oxygenase carbazole 1,9a-dioxygenase. Authors: Inoue, K. / Usami, Y. / Ashikawa, Y. / Noguchi, H. / Umeda, T. / Yamagami-Ashikawa, A. / Horisaki, T. / Uchimura, H. / Terada, T. / Nakamura, S. / Shimizu, K. / Habe, H. / Yamane, H. / Fujimoto, Z. / Nojiri, H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 317.7 KB | Display | ![]() |
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PDB format | ![]() | 255.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4nb8C ![]() 4nb9C ![]() 4nbaC ![]() 4nbcC ![]() 4nbdC ![]() 4nbeC ![]() 4nbfC ![]() 4nbgC ![]() 4nbhC ![]() 2de5S 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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Unit cell |
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Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 44896.711 Da / Num. of mol.: 3 / Mutation: I262V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 12448.059 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 800 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/9CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/OXY.gif)
![](data/chem/img/9CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-FES / #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1M ammonium acetate, 12.5% PEG 3350, 0.05M MES, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 7, 2006 |
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→50 Å / Num. obs: 110854 / % possible obs: 99.7 % / Biso Wilson estimate: 27.2 Å2 |
Reflection shell | Resolution: 2.05→2.12 Å / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DE5 Resolution: 2.05→33.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2213745.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.2898 Å2 / ksol: 0.351867 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.05→33.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.18 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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