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Yorodumi- PDB-7bui: Complex of reduced oxygenase and oxidized ferredoxin in carbazole... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bui | ||||||
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Title | Complex of reduced oxygenase and oxidized ferredoxin in carbazole 1,9a- dioxygenase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Rieske Iron-sulfur Protein | ||||||
Function / homology | Function and homology information carbazole catabolic process / : / organonitrogen compound catabolic process / ferredoxin hydrogenase activity / dioxygenase activity / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Janthinobacterium sp. Pseudomonas resinovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Matsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Complex of reduced oxygenase and oxidized ferredoxin in carbazole 1,9a- dioxygenase Authors: Matsuzawa, J. / Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bui.cif.gz | 296.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bui.ent.gz | 236.9 KB | Display | PDB format |
PDBx/mmJSON format | 7bui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/7bui ftp://data.pdbj.org/pub/pdb/validation_reports/bu/7bui | HTTPS FTP |
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-Related structure data
Related structure data | 2de5S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 5 molecules ABCDE
#1: Protein | Mass: 44910.738 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Janthinobacterium sp. (strain J3) (bacteria) Strain: J3 / Gene: carAa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84II6 #2: Protein | Mass: 12448.059 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas resinovorans (bacteria) / Gene: carAc / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GI16 |
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-Non-polymers , 5 types, 497 molecules
#3: Chemical | ChemComp-FES / #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.84 Å3/Da / Density % sol: 56.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Buffer: 50 mM Tris pH 7.5, 10% v/v glycerol, Reservior: 0.1 M sodium cacodylate pH 5.7, 14% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 90 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Nov 30, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→150 Å / Num. obs: 97397 / % possible obs: 99.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.15→2.19 Å / Num. unique obs: 4789 / CC1/2: 0.68 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DE5 Resolution: 2.15→62.17 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.621 / SU ML: 0.161 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.183 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 171.01 Å2 / Biso mean: 51.325 Å2 / Biso min: 24.5 Å2
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Refinement step | Cycle: final / Resolution: 2.15→62.17 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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