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Yorodumi- PDB-6evf: Structure of E285D S. cerevisiae Fdc1 with prFMN in the hydroxyla... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6evf | ||||||
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Title | Structure of E285D S. cerevisiae Fdc1 with prFMN in the hydroxylated form | ||||||
Components | Ferulic acid decarboxylase 1 | ||||||
Keywords | LYASE | ||||||
Function / homology | Function and homology information ferulate catabolic process / ferulate metabolic process / cinnamic acid catabolic process / phenacrylate decarboxylase / carboxy-lyase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | ||||||
Authors | Bailey, S.S. / David, L. / Payne, K.A.P. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6evf.cif.gz | 433.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6evf.ent.gz | 351 KB | Display | PDB format |
PDBx/mmJSON format | 6evf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ev/6evf ftp://data.pdbj.org/pub/pdb/validation_reports/ev/6evf | HTTPS FTP |
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-Related structure data
Related structure data | 6ev3C 6ev4C 6ev5C 6ev6C 6ev7C 6ev8C 6ev9C 6evaC 6evbC 6evcC 6evdC 6eveC 4zacS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 57046.535 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: FDC1, YDR539W, D3703.2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q03034, phenacrylate decarboxylase #2: Chemical | ChemComp-4LU / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-K / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.81 Å3/Da / Density % sol: 56.2 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→34.35 Å / Num. obs: 154138 / % possible obs: 99 % / Redundancy: 2.9 % / Net I/σ(I): 8.35 |
Reflection shell | Resolution: 2.06→3.134 Å / Redundancy: 2.9 % / Num. unique obs: 15457 / Rrim(I) all: 1.071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZAC Resolution: 2.06→34.35 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.284 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.154 / 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: 28.91 Å2
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Refinement step | Cycle: 1 / Resolution: 2.06→34.35 Å
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Refine LS restraints |
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