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- PDB-6ev3: Structure of wild type A. niger Fdc1 that has been illuminated wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ev3 | ||||||||||||
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Title | Structure of wild type A. niger Fdc1 that has been illuminated with UV light, with prFMN in the iminium and ketimine form | ||||||||||||
![]() | Ferulic acid decarboxylase 1 | ||||||||||||
![]() | LYASE | ||||||||||||
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 | ![]() ![]() ![]() | ||||||||||||
![]() | Bailey, S.S. / David, L. / Payne, K.A.P. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis. Authors: Bailey, S.S. / Payne, K.A.P. / Fisher, K. / Marshall, S.A. / Cliff, M.J. / Spiess, R. / Parker, D.A. / Rigby, S.E.J. / 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 | ![]() | 142.5 KB | Display | ![]() |
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PDB format | ![]() | 105.4 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 | ![]() | 29.2 KB | Display | |
Data in CIF | ![]() | 46.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ev4C ![]() 6ev5C ![]() 6ev6C ![]() 6ev7C ![]() 6ev8C ![]() 6ev9C ![]() 6evaC ![]() 6evbC ![]() 6evcC ![]() 6evdC ![]() 6eveC ![]() 6evfC ![]() 4za4S 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
-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, 740 molecules ![](data/chem/img/4LU.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/FZZ.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/K.gif)
![](data/chem/img/FZZ.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-4LU / | ||||
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#3: Chemical | ChemComp-MN / | ||||
#4: Chemical | #5: Chemical | ChemComp-FZZ / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 48.64 % |
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Crystal grow | Temperature: 277 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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 6, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→64.85 Å / Num. obs: 475106 / % possible obs: 96.4 % / Redundancy: 3.7 % / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.3→1.346 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 12466 / CC1/2: 0.5 / Rrim(I) all: 1.223 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZA4 Resolution: 1.3→64.85 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.244 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / 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: 14.446 Å2
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Refinement step | Cycle: 1 / Resolution: 1.3→64.85 Å
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Refine LS restraints |
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