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Yorodumi- PDB-6zh7: Crystal structure of fatty acid photodecarboxylase in the dark st... -
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-Basic information
Entry | Database: PDB / ID: 6zh7 | |||||||||
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Title | Crystal structure of fatty acid photodecarboxylase in the dark state determined by serial femtosecond crystallography at room temperature | |||||||||
Components | Fatty acid photodecarboxylase, chloroplastic | |||||||||
Keywords | OXIDOREDUCTASE / photoenzyme / XFEL / radiation damage free | |||||||||
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Hadjidemetriou, K. / Coquelle, N. / Weik, M. / Schlichting, I. / Barends, T.R.M. / Colletier, J.P. | |||||||||
Funding support | France, 2items
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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. #1: 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. / 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 | 6zh7.cif.gz | 242.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6zh7.ent.gz | 189.7 KB | Display | PDB format |
PDBx/mmJSON format | 6zh7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6zh7_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 6zh7_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6zh7_validation.xml.gz | 44.8 KB | Display | |
Data in CIF | 6zh7_validation.cif.gz | 64 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zh/6zh7 ftp://data.pdbj.org/pub/pdb/validation_reports/zh/6zh7 | HTTPS FTP |
-Related structure data
Related structure data | 6yruSC 6yrvC 6yrxC 6yrzC 6ys1C 6ys2C 7av4C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 77 - 643 / Label seq-ID: 1 - 567
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-Components
#1: Protein | Mass: 61116.598 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorella variabilis (plant) / Gene: FAP, CHLNCDRAFT_28598 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A248QE08, fatty acid photodecarboxylase #2: Chemical | #3: Chemical | ChemComp-STE / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 281.15 K / Method: batch mode / pH: 5.5 Details: 19% (w/v) PEG 4000, 0.1 M sodium citrate pH 5.5, 10 mM spermidine |
-Data collection
Diffraction | Mean temperature: 277.15 K / Serial crystal experiment: Y |
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Diffraction source | Source: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.3 Å |
Detector | Type: CS-PAD CXI-1 / Detector: PIXEL / Date: Nov 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2→25 Å / Num. obs: 93061 / % possible obs: 100 % / Redundancy: 355 % / CC1/2: 0.982 / CC star: 0.996 / R split: 0.151 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 236 % / Num. unique obs: 6086 / CC1/2: 0.548 / CC star: 0.841 / R split: 0.685 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6YRU Resolution: 2→24.95 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.893 / SU ML: 0.151 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.15 Å2 / Biso mean: 29.803 Å2 / Biso min: 11.55 Å2
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Refinement step | Cycle: final / Resolution: 2→24.95 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 18263 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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