[English] 日本語
Yorodumi- PDB-7r35: Difference-refined structure of fatty acid photodecarboxylase 300... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7r35 | ||||||
---|---|---|---|---|---|---|---|
Title | Difference-refined structure of fatty acid photodecarboxylase 300 ns 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, W. | ||||||
Funding support | 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7r35.cif.gz | 242.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7r35.ent.gz | 190.3 KB | Display | PDB format |
PDBx/mmJSON format | 7r35.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r35_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7r35_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7r35_validation.xml.gz | 47 KB | Display | |
Data in CIF | 7r35_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r3/7r35 ftp://data.pdbj.org/pub/pdb/validation_reports/r3/7r35 | HTTPS FTP |
-Related structure data
Related structure data | 7r33C 7r34C 7r36C 6zh7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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 | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.53 % |
---|---|
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 |
---|---|
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: 93055 / % possible obs: 100 % / Redundancy: 225 % / CC star: 0.992 / R split: 0.194 / Net I/σ(I): 4.4 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 149 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 6086 / CC star: 0.79 / R split: 0.845 / % possible all: 100 |
Serial crystallography sample delivery | Method: injection |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6ZH7 Resolution: 2→10 Å / SU ML: 0.57 / Cross valid method: THROUGHOUT / σ(F): 1.73 / Phase error: 49.01 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.15 Å2 / Biso mean: 30.7193 Å2 / Biso min: 3.49 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %
|