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Yorodumi- PDB-5gtg: Crystal structure of onion lachrymatory factor synthase (LFS) con... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gtg | |||||||||
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Title | Crystal structure of onion lachrymatory factor synthase (LFS) containing 1,2-propanediol | |||||||||
Components | Lachrymatory-factor synthase | |||||||||
Keywords | ISOMERASE / SRPBCC / helix-grip fold / cytosolic | |||||||||
Function / homology | lachrymatory-factor synthase / Polyketide cyclase/dehydrase / Polyketide cyclase / dehydrase and lipid transport / vacuole / START-like domain superfamily / trehalose / S-1,2-PROPANEDIOL / Lachrymatory-factor synthase Function and homology information | |||||||||
Biological species | Allium cepa (onion) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | |||||||||
Authors | Arakawa, T. / Sato, Y. / Takabe, J. / Masamura, N. / Tsuge, N. / Imai, S. / Fushinobu, S. | |||||||||
Citation | Journal: Acs Catalysis / Year: 2020 Title: Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase Authors: Arakawa, T. / Sato, Y. / Yamada, M. / Takabe, J. / Moriwaki, Y. / Masamura, N. / Kato, M. / Aoyagi, M. / Kamoi, T. / Terada, T. / Shimizu, K. / Tsuge, N. / Imai, S. / Fushinobu, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gtg.cif.gz | 263.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gtg.ent.gz | 210.3 KB | Display | PDB format |
PDBx/mmJSON format | 5gtg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gtg_validation.pdf.gz | 979.9 KB | Display | wwPDB validaton report |
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Full document | 5gtg_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5gtg_validation.xml.gz | 58.4 KB | Display | |
Data in CIF | 5gtg_validation.cif.gz | 80.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gt/5gtg ftp://data.pdbj.org/pub/pdb/validation_reports/gt/5gtg | HTTPS FTP |
-Related structure data
Related structure data | 5gteC 5gtfSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 9 molecules ABCDEFGH
#1: Protein | Mass: 19905.580 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Allium cepa (onion) / Gene: LFS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21AI References: UniProt: P59082, Isomerases; Intramolecular oxidoreductases #2: Polysaccharide | alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose | |
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-Non-polymers , 4 types, 591 molecules
#3: Chemical | ChemComp-PGO / #4: Chemical | #5: Chemical | ChemComp-MES / | #6: Water | ChemComp-HOH / | |
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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: 3.04 Å3/Da / Density % sol: 59.6 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Ammonium sulfate, MES / PH range: 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 95 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 23, 2016 | |||||||||||||||
Radiation | Monochromator: Numerical link type Si(111) double crystal monochromator, liquid nitrogen cooling Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.7→50 Å / Num. obs: 204662 / % possible obs: 97.3 % / Redundancy: 6.1 % / Net I/σ(I): 19.8 | |||||||||||||||
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.2 / CC1/2: 0.86 / % possible all: 79.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 5GTF Resolution: 1.7→47.94 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.887 / SU B: 1.58 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TWIN REFINEMENT HAS BEEN APPLIED
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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: 20.053 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→47.94 Å
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Refine LS restraints |
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