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- PDB-6r3n: Aspergillus niger ferulic acid decarboxylase (Fdc) in complex wit... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6r3n | |||||||||
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Title | Aspergillus niger ferulic acid decarboxylase (Fdc) in complex with the covalent adduct formed between prFMN cofactor and butynoic acid (Int1') | |||||||||
![]() | Ferulic acid decarboxylase 1 | |||||||||
![]() | LYASE / (de)carboxylase / UbiD / prFMN binding | |||||||||
Function / homology | ![]() styrene metabolic process / aromatic amino acid family catabolic process / phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / manganese ion binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Bailey, S.S. / Leys, D. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Atomic description of an enzyme reaction dependent on reversible 1,3-dipolar cycloaddition Authors: Bailey, S.S. / Payne, K.A.P. / Saaret, A. / Marshall, S.A. / Gostimskaya, I. / Kosov, I. / Fisher, K. / 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 | ![]() | 240.4 KB | Display | ![]() |
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PDB format | ![]() | 189 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 25.6 KB | Display | |
Data in CIF | ![]() | 39.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6r2pC ![]() 6r2rC ![]() 6r2tC ![]() 6r2zC ![]() 6r30C ![]() 6r32C ![]() 6r33C ![]() 6r34C ![]() 6r3fC ![]() 6r3gC ![]() 6r3iC ![]() 6r3jC ![]() 6r3lC ![]() 6r3oC ![]() 4za9S S: Starting model for refinement C: citing same article ( |
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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 A
#1: Protein | Mass: 56335.945 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 483 molecules ![](data/chem/img/JRK.gif)
![](data/chem/img/BYN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/BYN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-JRK / | ||
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#3: Chemical | ChemComp-BYN / | ||
#4: Chemical | ChemComp-MN / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M POTASSIUM THIOCYANATE, BIS-TRIS PROPANE 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 300K / Detector: PIXEL / Date: Jul 20, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.02→43.86 Å / Num. obs: 237279 / % possible obs: 87.03 % / Redundancy: 4.8 % / CC1/2: 0.995 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.02→1.056 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 3982 / CC1/2: 0.647 / % possible all: 14.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZA9 Resolution: 1.02→43.86 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.643 / SU ML: 0.015 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.971 Å2
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Refinement step | Cycle: LAST / Resolution: 1.02→43.86 Å
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Refine LS restraints |
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