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- PDB-6tic: Structure of A. niger Fdc I327S variant in complex with benzothio... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6tic | |||||||||
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Title | Structure of A. niger Fdc I327S variant in complex with benzothiophene 2 carboxylic acid | |||||||||
![]() | Ferulic acid decarboxylase 1 | |||||||||
![]() | LIGASE / (de)carboxylase / UbiD / aromatic acid / prFMN | |||||||||
Function / homology | ![]() phenacrylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Leys, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Enzymatic C-H activation of aromatic compounds through CO 2 fixation. Authors: Aleku, G.A. / Saaret, A. / Bradshaw-Allen, R.T. / Derrington, S.R. / Titchiner, G.R. / Gostimskaya, I. / Gahloth, D. / Parker, D.A. / Hay, S. / Leys, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6tibC ![]() 6tieC ![]() 6tihC ![]() 6tijC ![]() 6tilC ![]() 6tinC ![]() 6tioC ![]() 4zaaS 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 56309.867 Da / Num. of mol.: 1 / Mutation: I327S Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 556 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BYN.gif)
![](data/chem/img/ND8.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/BYN.gif)
![](data/chem/img/ND8.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-BYN / | #5: Chemical | ChemComp-ND8 / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium thiocyanate, Bis-Tris propane pH 6.5, 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.916 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→87.594 Å / Num. obs: 107134 / % possible obs: 94.6 % / Redundancy: 6.4 % / CC1/2: 1 / Rrim(I) all: 0.104 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.28→1.37 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 797 / CC1/2: 0.6 / Rrim(I) all: 1.116 / % possible all: 57.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZAA Resolution: 1.281→87.59 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.386 / SU ML: 0.059 / Cross valid method: FREE R-VALUE / ESU R: 0.064 / ESU R Free: 0.064 Details: Hydrogens have been added in their riding positions
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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 mean: 17.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.281→87.59 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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