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- PDB-6eve: Structure of R175A S. cerevisiae Fdc1 with prFMN in the iminium form -
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Open data
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Basic information
Entry | Database: PDB / ID: 6eve | ||||||
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Title | Structure of R175A S. cerevisiae Fdc1 with prFMN in the iminium form | ||||||
![]() | Ferulic acid decarboxylase 1 | ||||||
![]() | LYASE | ||||||
Function / homology | ![]() ferulate catabolic process / phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ubiquinone biosynthetic process / carboxy-lyase activity / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bailey, S.S. / David, L. | ||||||
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 | ![]() | 430.6 KB | Display | ![]() |
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PDB format | ![]() | 349.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 82.2 KB | Display | |
Data in CIF | ![]() | 119.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6ev3C ![]() 6ev4C ![]() 6ev5C ![]() 6ev6C ![]() 6ev7C ![]() 6ev8C ![]() 6ev9C ![]() 6evaC ![]() 6evbC ![]() 6evcC ![]() 6evdC ![]() 6evfC ![]() 4zacS 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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 56974.441 Da / Num. of mol.: 4 / Mutation: R175A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: FDC1, YDR539W, D3703.2 / Production host: ![]() ![]() #2: Chemical | ChemComp-4LU / #3: Chemical | ChemComp-MN / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium cacodylate pH 6.5, 0.25M Calcium Acetate, 15% PEG 4k |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→77.89 Å / Num. obs: 167153 / % possible obs: 100 % / Redundancy: 3.4 % / Net I/σ(I): 5.52 |
Reflection shell | Resolution: 2.05→2.134 Å / Redundancy: 2.9 % / Num. unique obs: 15457 / Rrim(I) all: 1.071 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4ZAC Resolution: 2.05→77.89 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.792 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.155 / 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: 27.333 Å2
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Refinement step | Cycle: 1 / Resolution: 2.05→77.89 Å
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Refine LS restraints |
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