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Yorodumi- PDB-6ll4: Oxygen-exposed carbazole-soaked reduced terminal oxygenase of car... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ll4 | ||||||
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Title | Oxygen-exposed carbazole-soaked reduced terminal oxygenase of carbazole 1,9a-dioxygenase | ||||||
Components | Terminal oxygenase component of carbazole | ||||||
Keywords | OXIDOREDUCTASE / ring-hydroxylating / dioxygenase / ligand-bound | ||||||
Function / homology | Function and homology information 2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Janthinobacterium sp. J3 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Oxygen-exposed carbazole-soaked reduced terminal oxygenase of carbazole 1,9a-dioxygenase with Authors: 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 | 6ll4.cif.gz | 262.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ll4.ent.gz | 208.7 KB | Display | PDB format |
PDBx/mmJSON format | 6ll4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/6ll4 ftp://data.pdbj.org/pub/pdb/validation_reports/ll/6ll4 | HTTPS FTP |
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-Related structure data
Related structure data | 1ww9S 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 , 1 types, 3 molecules ABC
#1: Protein | Mass: 44910.738 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Janthinobacterium sp. J3 (bacteria) / Strain: J3 / Gene: carAa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q84II6 |
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-Non-polymers , 10 types, 427 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EHX / ( | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-PGE / #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-MG / | #11: 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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.05 M MgCl2, 0.1 M HEPES ph 7.5 30% (v/v) PEG MME 550 |
-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 MX325HE / Detector: CCD / Date: Jul 19, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→200 Å / Num. obs: 58641 / % possible obs: 100 % / Redundancy: 13.7 % / Rmerge(I) obs: 0.372 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.2→2.24 Å / Num. unique obs: 2925 / CC1/2: 0.597 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WW9 Resolution: 2.2→48.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.809 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.319 / ESU R Free: 0.232 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: 101.54 Å2 / Biso mean: 35.214 Å2 / Biso min: 13.59 Å2
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Refinement step | Cycle: final / Resolution: 2.2→48.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.255 Å / Rfactor Rfree error: 0
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