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- PDB-3vmi: Carbazole- and oxygen-bound complex between oxygenase and ferredo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vmi | ||||||
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Title | Carbazole- and oxygen-bound complex between oxygenase and ferredoxin in carbazole 1,9a-dioxygenase | ||||||
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![]() | OXIDOREDUCTASE / Catalytic mechanism / Electron transfer complex / Rieske nonheme iron oxygenase system / Terminal oxygenase / Rieske-type ferredoxin / 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. / Nojiri, H. | ||||||
![]() | ![]() Title: Structural insight into the substrate- and dioxygenbinding manner in the catalytic cycle of rieske nonheme iron oxygenase system, carbazole 1,9adioxygenase Authors: Ashikawa, Y. / Fujimoto, Z. / Usami, Y. / Inoue, K. / Noguchi, H. / Yamane, H. / 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 | ![]() | 319.1 KB | Display | ![]() |
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PDB format | ![]() | 255.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3vmgC ![]() 3vmhC ![]() 2de7S 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: 44910.738 Da / Num. of mol.: 3 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, 865 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: 2.59 Å3/Da / Density % sol: 52.57 % |
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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 Bis-Tris, 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 315 / Detector: CCD / Date: Jun 28, 2005 |
Radiation | Monochromator: Rotated-inclined 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→50 Å / Num. obs: 117108 / % possible obs: 99.3 % / Biso Wilson estimate: 26.9 Å2 / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.312 / Num. unique all: 11459 / % possible all: 97.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2DE7 Resolution: 2→32.68 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2192879.45 / 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: 40.4459 Å2 / ksol: 0.344831 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→32.68 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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