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Open data
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Basic information
Entry | Database: PDB / ID: 6yrz | ||||||
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Title | Crystal structure of FAP et pH 8.5 after illumination at 150K | ||||||
![]() | Fatty acid photodecarboxylase, chloroplastic | ||||||
![]() | BIOSYNTHETIC PROTEIN / GMC fold | ||||||
Function / homology | ![]() fatty acid photodecarboxylase / choline dehydrogenase activity / glycine betaine biosynthetic process from choline / chloroplast / flavin adenine dinucleotide binding / mitochondrial inner membrane / lyase activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sorigue, D. / Legrand, P. / Blangy, S. / Beisson, F. / Arnoux, P. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Mechanism and dynamics of fatty acid photodecarboxylase. Authors: Sorigue, D. / Hadjidemetriou, K. / Blangy, S. / Gotthard, G. / Bonvalet, A. / Coquelle, N. / Samire, P. / Aleksandrov, A. / Antonucci, L. / Benachir, A. / Boutet, S. / Byrdin, M. / ...Authors: Sorigue, D. / Hadjidemetriou, K. / Blangy, S. / Gotthard, G. / Bonvalet, A. / Coquelle, N. / Samire, P. / Aleksandrov, A. / Antonucci, L. / Benachir, A. / Boutet, S. / Byrdin, M. / Cammarata, M. / Carbajo, S. / Cuine, S. / Doak, R.B. / Foucar, L. / Gorel, A. / Grunbein, M. / Hartmann, E. / Hienerwadel, R. / Hilpert, M. / Kloos, M. / Lane, T.J. / Legeret, B. / Legrand, P. / Li-Beisson, Y. / Moulin, S.L.Y. / Nurizzo, D. / Peltier, G. / Schiro, G. / Shoeman, R.L. / Sliwa, M. / Solinas, X. / Zhuang, B. / Barends, T.R.M. / Colletier, J.P. / Joffre, M. / Royant, A. / Berthomieu, C. / Weik, M. / Domratcheva, T. / Brettel, K. / Vos, M.H. / Schlichting, I. / Arnoux, P. / Muller, P. / Beisson, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.5 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6yruSC ![]() 6yrvC ![]() 6yrxC ![]() 6ys1C ![]() 6ys2C ![]() 6zh7C ![]() 7av4C S: Starting model for refinement C: citing same article ( |
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Similar structure data | |
Experimental dataset #1 | Data reference: ![]() |
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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
-Protein , 1 types, 1 molecules AAA
#1: Protein | Mass: 61086.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: A0A248QE08, fatty acid photodecarboxylase |
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-Non-polymers , 6 types, 445 molecules ![](data/chem/img/FAD.gif)
![](data/chem/img/PJ8.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/STE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PJ8.gif)
![](data/chem/img/CO2.gif)
![](data/chem/img/STE.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-FAD / |
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#3: Chemical | ChemComp-PJ8 / |
#4: Chemical | ChemComp-CO2 / |
#5: Chemical | ChemComp-STE / |
#6: Chemical | ChemComp-1PE / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.5 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM |
-Data collection
Diffraction | Mean temperature: 150 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Sep 28, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.82→87 Å / Num. obs: 66267 / % possible obs: 99.7 % / Redundancy: 13.518 % / Biso Wilson estimate: 37.236 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.089 / Χ2: 1.188 / Net I/σ(I): 18.38 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6YRU Resolution: 1.824→46.819 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.182 / WRfactor Rwork: 0.152 / SU B: 2.564 / SU ML: 0.074 / Average fsc free: 0.9205 / Average fsc work: 0.931 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.096 Details: Hydrogens have been added in their 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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.727 Å2
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Refinement step | Cycle: LAST / Resolution: 1.824→46.819 Å
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Refine LS restraints |
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LS refinement shell |
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