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Yorodumi- PDB-7av4: Dark state structure of the C432S mutant of Fatty Acid Photodecar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7av4 | ||||||
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Title | Dark state structure of the C432S mutant of Fatty Acid Photodecarboxylase (FAP) | ||||||
Components | Fatty acid photodecarboxylase, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / Active site mutation dark state | ||||||
Function / homology | Function and homology information 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 | Chlorella variabilis (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.936 Å | ||||||
Authors | Schlichting, I. / Hartmann, E. / Arnoux, P. / Sorigue, D. / Beisson, F. | ||||||
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. #1: Journal: Science / Year: 2017 Title: An algal photoenzyme converts fatty acids to hydrocarbons. Authors: Sorigue, D. / Legeret, B. / Cuine, S. / Blangy, S. / Moulin, S. / Billon, E. / Richaud, P. / Brugiere, S. / Coute, Y. / Nurizzo, D. / Muller, P. / Brettel, K. / Pignol, D. / Arnoux, P. / Li- ...Authors: Sorigue, D. / Legeret, B. / Cuine, S. / Blangy, S. / Moulin, S. / Billon, E. / Richaud, P. / Brugiere, S. / Coute, Y. / Nurizzo, D. / Muller, P. / Brettel, K. / Pignol, D. / Arnoux, P. / Li-Beisson, Y. / Peltier, G. / Beisson, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7av4.cif.gz | 138.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7av4.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7av4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7av4_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 7av4_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 7av4_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 7av4_validation.cif.gz | 38.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/7av4 ftp://data.pdbj.org/pub/pdb/validation_reports/av/7av4 | HTTPS FTP |
-Related structure data
Related structure data | 6yruSC 6yrvC 6yrxC 6yrzC 6ys1C 6ys2C 6zh7C 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: 68888.461 Da / Num. of mol.: 1 / Mutation: C432S, Nterminal truncation Source method: isolated from a genetically manipulated source Details: N-terminal truncation Mutation C432S / Source: (gene. exp.) Chlorella variabilis (plant) / Gene: FAP, CHLNCDRAFT_28598 / Production host: Escherichia coli (E. coli) References: UniProt: A0A248QE08, fatty acid photodecarboxylase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-FAD / | #4: Chemical | #5: 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: 3.17 Å3/Da / Density % sol: 61.2 % / Description: rhomboid |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: ~ 20-30 % PEG 4000, 0.1 M Citrate pH5.5, 10 mM spermidine |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.936→86.956 Å / Num. all: 216366 / Num. obs: 56924 / % possible obs: 99.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 39.5 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.097 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.936→2.05 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1 / Num. unique obs: 8961 / CC1/2: 0.54 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6yru Resolution: 1.936→46.731 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.271 / SU ML: 0.11 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.123 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: 36.163 Å2
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Refinement step | Cycle: LAST / Resolution: 1.936→46.731 Å
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Refine LS restraints |
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LS refinement shell |
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