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- PDB-8crd: Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8crd | ||||||
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Title | Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) variant in complex with prenylated flavin hydroxylated at the C1 prime position | ||||||
![]() | Ferulic acid decarboxylase 1 | ||||||
![]() | LYASE / Decarboxylase / prFMN | ||||||
Function / homology | ![]() styrene metabolic process / aromatic amino acid family catabolic process / phenacrylate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / manganese ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Roberts, G.W. / Leys, D. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Aspergillus niger ferulic acid decarboxylase (Fdc) T40C-S315C (DB1) variant in complex with prenylated flavin hydroxylated at the C1 prime position Authors: Roberts, G.W. / 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 | ![]() | 132.4 KB | Display | ![]() |
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PDB format | ![]() | 98.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 755.8 KB | Display | ![]() |
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Full document | ![]() | 758.8 KB | Display | |
Data in XML | ![]() | 25.5 KB | Display | |
Data in CIF | ![]() | 39.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oedC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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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 A
#1: Protein | Mass: 56354.047 Da / Num. of mol.: 1 / Mutation: T40C S315C Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 560 molecules ![](data/chem/img/BYN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/SCN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-BYN / | ||||
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#3: Chemical | ChemComp-MN / | ||||
#4: Chemical | #5: Chemical | ChemComp-SCN / #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: 48.48 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: BIS-TRIS propane, potassium thiocyanate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 11, 2021 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→53.29 Å / Num. obs: 110958 / % possible obs: 93.5 % / Redundancy: 13.3 % / CC1/2: 1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.35→1.37 Å / Redundancy: 10.6 % / Num. unique obs: 3493 / CC1/2: 0.3 / % possible all: 59.6 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.14 Å2
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Refinement step | Cycle: 1 / Resolution: 1.35→53.29 Å
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Refine LS restraints |
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