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Yorodumi- PDB-6llk: Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6llk | ||||||
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Title | Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase | ||||||
Components | Terminal oxygenase component of carbazole | ||||||
Keywords | OXIDOREDUCTASE / 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. | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H. | ||||||
Funding support | Japan, 1items
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Citation | Journal: To Be Published Title: Biphenyl-2,2',3-triol-soaked terminal oxygenase of carbazole 1,9a-dioxygenase 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 | 6llk.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6llk.ent.gz | 75.9 KB | Display | PDB format |
PDBx/mmJSON format | 6llk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6llk_validation.pdf.gz | 783.3 KB | Display | wwPDB validaton report |
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Full document | 6llk_full_validation.pdf.gz | 785.9 KB | Display | |
Data in XML | 6llk_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 6llk_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ll/6llk ftp://data.pdbj.org/pub/pdb/validation_reports/ll/6llk | HTTPS FTP |
-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, 1 molecules A
#1: Protein | Mass: 44910.738 Da / Num. of mol.: 1 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 |
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-Non-polymers , 6 types, 284 molecules
#2: Chemical | ChemComp-FES / |
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#3: Chemical | ChemComp-FE2 / |
#4: Chemical | ChemComp-WBP / |
#5: Chemical | ChemComp-DMS / |
#6: Chemical | ChemComp-MPD / ( |
#7: Water | ChemComp-HOH / |
-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: 4.21 Å3/Da / Density % sol: 70.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M MES pH 6.2, 15-17.5% MPD |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.16→50 Å / Num. obs: 33834 / % possible obs: 100 % / Redundancy: 22.4 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 1.353 / Num. unique obs: 33834 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WW9 Resolution: 2.3→29.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 4.241 / SU ML: 0.102 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.157 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: 112.07 Å2 / Biso mean: 35.695 Å2 / Biso min: 16.17 Å2
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Refinement step | Cycle: final / Resolution: 2.3→29.39 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Rfactor Rfree error: 0
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