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Yorodumi- PDB-5xj8: Crystal structure of PlsY (YgiH), an integral membrane glycerol 3... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xj8 | |||||||||||||||||||||
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Title | Crystal structure of PlsY (YgiH), an integral membrane glycerol 3-phosphate acyltransferase - the lysphosphatidic acid form | |||||||||||||||||||||
Components | Glycerol-3-phosphate acyltransferase | |||||||||||||||||||||
Keywords | TRANSFERASE / 1-hexadecanoyl-sn-glycero-3-phosphate / 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphate / glycerylphosphate acyltransferase / GPAT / in meso / lipid cubic phase / lipidic cubic phase / lipid metabolism / LPA / lysophophatidic acid / lyso PA / lysoPA / 16:0 lyso PA / monoacylglycerol / palmitoyl lysophosphatidic acid / PA(16:0/0:0) / phospholipid biosynthesis / PlsY / 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: 2.41 Å | |||||||||||||||||||||
Authors | Li, Z. / Tang, Y. / Li, D. | |||||||||||||||||||||
Funding support | China, 6items
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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 | 5xj8.cif.gz | 88.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xj8.ent.gz | 66.5 KB | Display | PDB format |
PDBx/mmJSON format | 5xj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xj8_validation.pdf.gz | 669.7 KB | Display | wwPDB validaton report |
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Full document | 5xj8_full_validation.pdf.gz | 672.6 KB | Display | |
Data in XML | 5xj8_validation.xml.gz | 15.6 KB | Display | |
Data in CIF | 5xj8_validation.cif.gz | 20.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xj/5xj8 ftp://data.pdbj.org/pub/pdb/validation_reports/xj/5xj8 | 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.: 2 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 #2: Chemical | #3: Chemical | ChemComp-NKO / ( | #4: 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: 2.64 Å3/Da / Density % sol: 53.41 % |
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Crystal grow | Temperature: 293 K / Method: lipidic cubic phase / pH: 8 Details: 1mol% of palmitoyl lysophosphatidic acid, 39% PEG 350 MME, 0.04M NaCl, 0.04M Tris HCl pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.41→35.33 Å / Num. obs: 18124 / % possible obs: 99.1 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.06 / Net I/σ(I): 11.37 |
Reflection shell | Resolution: 2.41→2.5 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / Rpim(I) all: 0.448 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.41→35.33 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.41→35.33 Å
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Refine LS restraints |
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LS refinement shell |
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