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- PDB-6llh: Biphenyl-2,3-diol-soaked resting complex of Oxy and Fd in carbazo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6llh | ||||||
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Title | Biphenyl-2,3-diol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase | ||||||
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![]() | OXIDOREDUCTASE / complex / dioxygenase / ligand-bound | ||||||
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 | Janthinobacterium sp.![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wang, Y.X. / Suzuki-Minakuchi, C. / Nojiri, H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Biphenyl-2,2',3-triol-soaked resting complex of Oxy and Fd in carbazole 1,9a-dioxygenase Authors: Wang, Y.X. / Suzuki-Minakuchi, C. / 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 | ![]() | 334.5 KB | Display | ![]() |
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PDB format | ![]() | 267.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6llfC ![]() 2de5S 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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1 |
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Unit cell |
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Components
-Protein , 2 types, 6 molecules ABCDEF
#1: Protein | Mass: 44910.738 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: J3 / Gene: carAa / Production host: ![]() ![]() #2: Protein | Mass: 12448.059 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 9 types, 1069 molecules ![](data/chem/img/FE2.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/BPY.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FES.gif)
![](data/chem/img/BPY.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-FES / #5: Chemical | #6: Chemical | ChemComp-EDO / #7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Chemical | #10: Chemical | ChemComp-GOL / | #11: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.05 M Bis-Tris pH 5.5, 0.1 M Ammonium Acetate, 12.5% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 9, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. obs: 121104 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2→2.03 Å / Num. unique obs: 121194 / CC1/2: 0.876 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DE5 Resolution: 1.99→36.59 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.549 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.143 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: 98.7 Å2 / Biso mean: 30.155 Å2 / Biso min: 11.68 Å2
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Refinement step | Cycle: final / Resolution: 1.99→36.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.993→2.045 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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