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Open data
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Basic information
Entry | Database: PDB / ID: 6evb | ||||||
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Title | Structure of E282Q A. niger Fdc1 with prFMN in the iminium form | ||||||
![]() | Ferulic acid decarboxylase 1 | ||||||
![]() | LYASE | ||||||
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. / 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 | ![]() | 139.4 KB | Display | ![]() |
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PDB format | ![]() | 103.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 770.5 KB | Display | ![]() |
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Full document | ![]() | 784.7 KB | Display | |
Data in XML | ![]() | 29 KB | Display | |
Data in CIF | ![]() | 46.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ev3C ![]() 6ev4C ![]() 6ev5C ![]() 6ev6C ![]() 6ev7C ![]() 6ev8C ![]() 6ev9C ![]() 6evaC ![]() 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 on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 56334.961 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 702 molecules ![](data/chem/img/4LU.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-4LU / | ||||
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#3: Chemical | ChemComp-MN / | ||||
#4: Chemical | #5: Chemical | ChemComp-SCN / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.35 % |
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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 PILATUS3 S 6M / Detector: PIXEL / Date: Feb 2, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→47.99 Å / Num. obs: 200417 / % possible obs: 100 % / Redundancy: 7 % / Net I/σ(I): 13.99 |
Reflection shell | Resolution: 1.13→1.17 Å / Redundancy: 6.6 % / Num. unique obs: 19595 / Rrim(I) all: 0.6468 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZA4 Resolution: 1.13→47.99 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.424 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.029 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.371 Å2
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Refinement step | Cycle: 1 / Resolution: 1.13→47.99 Å
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Refine LS restraints |
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