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- PDB-2de7: The substrate-bound complex between oxygenase and ferredoxin in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2de7 | ||||||
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Title | The substrate-bound complex between oxygenase and ferredoxin in carbazole 1,9a-dioxygenase | ||||||
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![]() | OXIDOREDUCTASE / Electron transfer complex / Rieske non-heme 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: Electron Transfer Complex Formation between Oxygenase and Ferredoxin Components in Rieske Nonheme Iron Oxygenase System Authors: Ashikawa, Y. / Fujimoto, Z. / Noguchi, H. / Habe, H. / Omori, T. / 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 | ![]() | 322.1 KB | Display | ![]() |
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PDB format | ![]() | 257.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 507.1 KB | Display | ![]() |
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Full document | ![]() | 533.6 KB | Display | |
Data in XML | ![]() | 63.5 KB | Display | |
Data in CIF | ![]() | 91.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2de5C ![]() 2de6C ![]() 1vckS ![]() 1ww9S 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.) ![]() ![]() ![]() References: GenBank: 28201207, UniProt: Q84II6*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation ...References: GenBank: 28201207, UniProt: Q84II6*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor #2: Protein | Mass: 12448.059 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: GenBank: 27228521, UniProt: Q8GI16*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation ...References: GenBank: 27228521, UniProt: Q8GI16*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donor |
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-Non-polymers , 4 types, 989 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/9CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/9CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-FES / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.3 % |
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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 4 / Detector: CCD / Date: Nov 27, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.91 Å / Num. obs: 118094 / % possible obs: 100 % / Biso Wilson estimate: 18.2 Å2 |
Reflection shell | Resolution: 2→2.07 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1vck, 1ww9 Resolution: 2→41.91 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1977695.53 / 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: 41.9975 Å2 / ksol: 0.358316 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→41.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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