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Yorodumi- PDB-4zac: Structure of S. cerevisiae Fdc1 with the prenylated-flavin cofact... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zac | ||||||
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Title | Structure of S. cerevisiae Fdc1 with the prenylated-flavin cofactor in the iminium form. | ||||||
Components | Ferulic acid decarboxylase 1 | ||||||
Keywords | LYASE / (de)carboxylase / prenylated flavin binding / UbiD-type enzyme | ||||||
Function / homology | Function and homology information 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 | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | White, M.D. / Leys, D. | ||||||
Citation | Journal: Nature / Year: 2015 Title: New cofactor supports alpha , beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Authors: Payne, K.A. / White, M.D. / Fisher, K. / Khara, B. / Bailey, S.S. / Parker, D. / Rattray, N.J. / Trivedi, D.K. / Goodacre, R. / Beveridge, R. / Barran, P. / Rigby, S.E. / Scrutton, N.S. / Hay, S. / Leys, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zac.cif.gz | 443.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zac.ent.gz | 358.5 KB | Display | PDB format |
PDBx/mmJSON format | 4zac.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zac_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 4zac_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 4zac_validation.xml.gz | 89.7 KB | Display | |
Data in CIF | 4zac_validation.cif.gz | 130.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/za/4zac ftp://data.pdbj.org/pub/pdb/validation_reports/za/4zac | HTTPS FTP |
-Related structure data
Related structure data | 4za4SC 4za5C 4za7C 4za8C 4za9C 4zaaC 4zabC 4zadC 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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3 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 56231.676 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Gene: FDC1, YDR539W, D3703.2 / Production host: Escherichia coli (E. coli) References: UniProt: Q03034, Lyases; Carbon-carbon lyases; Carboxy-lyases |
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-Non-polymers , 5 types, 1462 molecules
#2: Chemical | #3: Chemical | ChemComp-K / #4: Chemical | ChemComp-MN / #5: Chemical | ChemComp-4LU / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.83 Å3/Da / Density % sol: 56.6 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: crystals were obtained in 0.2M calcium acetate, 20% PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.98 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→54.19 Å / Num. obs: 282233 / % possible obs: 98.8 % / Redundancy: 3.7 % / Rpim(I) all: 0.039 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.392 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4ZA4 Resolution: 1.65→54.19 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.642 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.081 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.852 Å2
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Refinement step | Cycle: 1 / Resolution: 1.65→54.19 Å
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Refine LS restraints |
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