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Yorodumi- PDB-4nbg: Oxygenase with Gln282 replaced by Tyr and ferredoxin complex of c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nbg | ||||||
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Title | Oxygenase with Gln282 replaced by Tyr and ferredoxin complex of carbazole 1,9a-dioxygenase | ||||||
Components |
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Keywords | OXIDOREDUCTASE / Rieske non-heme iron oxygenase / carbazole 1 / 9a-dioxygenase | ||||||
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 (bacteria) Pseudomonas resinovorans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Ashikawa, Y. / Usami, Y. / Inoue, K. / Nojiri, H. | ||||||
Citation | Journal: Appl.Environ.Microbiol. / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4nbg.cif.gz | 324.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nbg.ent.gz | 261 KB | Display | PDB format |
PDBx/mmJSON format | 4nbg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nb/4nbg ftp://data.pdbj.org/pub/pdb/validation_reports/nb/4nbg | HTTPS FTP |
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-Related structure data
Related structure data | 4nb8C 4nb9C 4nbaC 4nbbC 4nbcC 4nbdC 4nbeC 4nbfC 4nbhC 2de5S C: citing same article (ref.) 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
#1: Protein | Mass: 44945.781 Da / Num. of mol.: 3 / Mutation: Q282Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Janthinobacterium (bacteria) / Strain: J3 / Gene: carAa / Plasmid: pEQ282Y / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q84II6, EC: 1.14.12.22 #2: Protein | Mass: 12448.059 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas resinovorans (bacteria) / Strain: CA10 / Gene: carAc / Plasmid: pECAC1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8GI16, EC: 1.14.12.22 #3: Chemical | #4: Chemical | ChemComp-FES / #5: Water | ChemComp-HOH / | |
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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: 2.62 Å3/Da / Density % sol: 53.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: 0.1M ammonium acetate, 12.5% PEG 3350, 0.05M MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 16, 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: 1.85→50 Å / Num. obs: 151228 / % possible obs: 100 % / Biso Wilson estimate: 15.8 Å2 |
Reflection shell | Resolution: 1.85→1.92 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2DE5 Resolution: 1.85→39.22 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2478496.68 / 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: 39.2798 Å2 / ksol: 0.34795 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→39.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
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Xplor file |
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