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Yorodumi- PDB-7r34: Difference-refined structure of fatty acid photodecarboxylase 900... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r34 | ||||||
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Title | Difference-refined structure of fatty acid photodecarboxylase 900 ps following 400-nm laser irradiation of the dark-state determined by SFX | ||||||
Components | Fatty acid photodecarboxylase, chloroplastic | ||||||
Keywords | OXIDOREDUCTASE / Fatty acid decarboxylation | ||||||
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. / Barends, T.R.M. / De Zitter, E. / Schlichting, I. / Colletier, J.P. / Weik, M. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Time-resolved serial femtosecond crystallography on fatty-acid photodecarboxylase: lessons learned. Authors: Hadjidemetriou, K. / Coquelle, N. / Barends, T.R.M. / De Zitter, E. / Schlichting, I. / Colletier, J.P. / Weik, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r34.cif.gz | 242.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r34.ent.gz | 190.6 KB | Display | PDB format |
PDBx/mmJSON format | 7r34.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r34_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 7r34_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 7r34_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 7r34_validation.cif.gz | 65.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/7r34 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/7r34 | HTTPS FTP |
-Related structure data
Related structure data | 7r33C 7r35C 7r36C 6zh7S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.11577/1775333 / Data set type: diffraction image data Details: https://cxidb.org/data/177/FAP_900ps/ and https://cxidb.org/id-177.html |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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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: 93064 / % possible obs: 100 % / Redundancy: 270 % / CC1/2: 0.994 / R split: 0.18 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 179 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6086 / CC star: 0.797 / R split: 0.8 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZH7 Resolution: 2→10 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.71 / Phase error: 46.49 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.65 Å2 / Biso mean: 34.4324 Å2 / Biso min: 6.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→10 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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