+Open data
-Basic information
Entry | Database: PDB / ID: 6yru | ||||||
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Title | Crystal structure of FAP in the dark at 100K | ||||||
Components | Fatty acid Photodecarboxylase | ||||||
Keywords | BIOSYNTHETIC PROTEIN / GMC fold | ||||||
Function / homology | Function and homology information choline dehydrogenase activity / fatty acid photodecarboxylase / glycine betaine biosynthetic process from choline / chloroplast / flavin adenine dinucleotide binding / mitochondrial inner membrane / lyase activity Similarity search - Function | ||||||
Biological species | Chlorella variabilis (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å | ||||||
Authors | Sorigue, D. / Gotthard, G. / Blangy, S. / Nurizzo, D. / Royant, A. / Beisson, F. / Arnoux, P. | ||||||
Funding support | France, 1items
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Citation | Journal: Science / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yru.cif.gz | 143 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yru.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6yru.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yru ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yru | HTTPS FTP |
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-Related structure data
Related structure data | 6yrvC 6yrxC 6yrzC 6ys1C 6ys2C 6zh7C 7av4C 5nccS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.11577/1775333 / Data set type: diffraction image data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 61086.574 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella variabilis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2D0TC92 | ||||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.79 % |
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Crystal grow | Temperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: PEG 4000 25-40%, Na citrate 100 mM, spermidine 10mM |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97372 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 10, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97372 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.78→86 Å / Num. obs: 69240 / % possible obs: 99.3 % / Redundancy: 4.727 % / Biso Wilson estimate: 34.226 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.096 / Χ2: 1.016 / Net I/σ(I): 11.02 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5NCC Resolution: 1.78→46.503 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 3.45 / SU ML: 0.096 / Cross valid method: FREE R-VALUE / ESU R: 0.102 / ESU R Free: 0.1 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.186 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→46.503 Å
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Refine LS restraints |
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LS refinement shell |
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