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- PDB-4zad: Structure of C. dubliensis Fdc1 with the prenylated-flavin cofact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zad | ||||||
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Title | Structure of C. dubliensis Fdc1 with the prenylated-flavin cofactor in the iminium form. | ||||||
![]() | Fdc1 | ||||||
![]() | LYASE / (de)carboxylase / prenylated flavin binding / UbiD-type enzyme | ||||||
Function / homology | ![]() phenacrylate decarboxylase / ferulate metabolic process / cinnamic acid catabolic process / carboxy-lyase activity / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Bailey, S.S. / Leys, D. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 215.5 KB | Display | ![]() |
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PDB format | ![]() | 170.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 38.5 KB | Display | |
Data in CIF | ![]() | 52.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4za4C ![]() 4za5C ![]() 4za7C ![]() 4za8C ![]() 4za9C ![]() 4zaaC ![]() 4zabC ![]() 4zacC 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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Unit cell |
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Components
#1: Protein | Mass: 57737.922 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 0.2 M potassium thiocyanate, sodium acetate pH 5.5 and 15% w/v PEG 4000. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→67.04 Å / Num. obs: 39186 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rpim(I) all: 0.091 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 2.46→2.52 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.48 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]()
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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: 26.035 Å2
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Refinement step | Cycle: LAST / Resolution: 2.46→67.04 Å
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Refine LS restraints |
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