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- PDB-2de5: Crystal structure of the electron transfer complex between oxygen... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2de5 | ||||||
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Title | Crystal structure of the electron transfer 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 | ![]() | 323.4 KB | Display | ![]() |
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PDB format | ![]() | 260.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2de6C ![]() 2de7C ![]() 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
#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 #3: Chemical | #4: Chemical | ChemComp-FES / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1-2mM sodium dithionite, 14% PEG MME 2000, 0.05M Bis-Tris, pH 6.5, 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: Feb 6, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→44.92 Å / Num. obs: 138880 / % possible obs: 99.7 % / Biso Wilson estimate: 23.2 Å2 |
Reflection shell | Resolution: 1.9→1.97 Å / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1vck, 1ww9 Resolution: 1.9→44.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2218424.97 / 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: 53.4574 Å2 / ksol: 0.374991 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→44.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→2.02 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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