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Yorodumi- PDB-5xj6: Crystal structure of PlsY (YgiH), an integral membrane glycerol 3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xj6 | ||||||||||||||||||
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Title | Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the glycerol 3-phosphate form | ||||||||||||||||||
Components | Glycerol-3-phosphate acyltransferase | ||||||||||||||||||
Keywords | TRANSFERASE / glycerol 3-phosphate acyltransferase / glycerylphosphate acyltransferase / GPAT / in meso / lipid cubic phase / lipidic cubic phase / lipid metabolism / monoacylglycerol / phospholipid biosynthesis / PlsY / substrate / YgiH | ||||||||||||||||||
Function / homology | Function and homology information acyl phosphate:glycerol-3-phosphate acyltransferase / acyl-phosphate glycerol-3-phosphate acyltransferase activity / phospholipid biosynthetic process / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å | ||||||||||||||||||
Authors | Li, Z. / Tang, Y. / Li, D. | ||||||||||||||||||
Funding support | China, 5items
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Citation | Journal: Nat Commun / Year: 2017 Title: Structural insights into the committed step of bacterial phospholipid biosynthesis. Authors: Li, Z. / Tang, Y. / Wu, Y. / Zhao, S. / Bao, J. / Luo, Y. / Li, D. | ||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xj6.cif.gz | 56.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xj6.ent.gz | 39.4 KB | Display | PDB format |
PDBx/mmJSON format | 5xj6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xj6_validation.pdf.gz | 881.1 KB | Display | wwPDB validaton report |
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Full document | 5xj6_full_validation.pdf.gz | 877.1 KB | Display | |
Data in XML | 5xj6_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 5xj6_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/5xj6 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/5xj6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21892.002 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: plsY, aq_676 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: O66905, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups | ||||
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#2: Chemical | ChemComp-G3P / | ||||
#3: Chemical | ChemComp-OLC / ( #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.8 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 35-38% PEG 400, 0.1-0.2M LiCl, 0.1M Tris HCl pH 8.0, 80mM glycerol phosphate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.37→45.84 Å / Num. obs: 8548 / % possible obs: 98.9 % / Redundancy: 12.4 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.06 / Net I/σ(I): 11.9 |
Reflection shell | Resolution: 2.37→2.46 Å / Redundancy: 9.7 % / Rmerge(I) obs: 1.145 / Mean I/σ(I) obs: 1.7 / Rpim(I) all: 0.382 / % possible all: 89.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→45.84 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.32
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.37→45.84 Å
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Refine LS restraints |
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LS refinement shell |
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