+Open data
-Basic information
Entry | Database: PDB / ID: 5jwy | ||||||
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Title | Structure of lipid phosphate phosphatase PgpB complex with PE | ||||||
Components | Phosphatidylglycerophosphatase B | ||||||
Keywords | HYDROLASE / transmembrane helices / protein-lipid complex / enzyme | ||||||
Function / homology | Function and homology information diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / phosphatidate phosphatase activity / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / phosphatidylglycerol biosynthetic process / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process ...diacylglycerol diphosphate phosphatase / diacylglycerol diphosphate phosphatase activity / phosphatidate phosphatase / phosphatidate phosphatase activity / phosphatidylglycerophosphatase / undecaprenyl-diphosphate phosphatase / undecaprenyl-diphosphatase activity / phosphatidylglycerol biosynthetic process / phosphatidylglycerophosphatase activity / glycerophospholipid biosynthetic process / phospholipid catabolic process / plasma membrane => GO:0005886 / peptidoglycan biosynthetic process / cell outer membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å | ||||||
Authors | Tong, S. / Wang, M. / Zheng, L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Structural Insight into Substrate Selection and Catalysis of Lipid Phosphate Phosphatase PgpB in the Cell Membrane. Authors: Tong, S. / Lin, Y. / Lu, S. / Wang, M. / Bogdanov, M. / Zheng, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jwy.cif.gz | 63.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jwy.ent.gz | 49.7 KB | Display | PDB format |
PDBx/mmJSON format | 5jwy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jw/5jwy ftp://data.pdbj.org/pub/pdb/validation_reports/jw/5jwy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29946.375 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pgpB, b1278, JW1270 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) References: UniProt: P0A924, phosphatidylglycerophosphatase, diacylglycerol diphosphate phosphatase, phosphatidate phosphatase, undecaprenyl-diphosphate phosphatase |
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#2: Chemical | ChemComp-46E / ( |
#3: 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: 3.21 Å3/Da / Density % sol: 61.66 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG6000, sodium chloride, ADA |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9794 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 14 % / Number: 95967 / Rsym value: 0.102 / D res high: 3.2 Å / D res low: 132.095 Å / Num. obs: 6838 / % possible obs: 100 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 3.2→132.1 Å / Num. obs: 6838 / % possible obs: 100 % / Redundancy: 14 % / Rsym value: 0.102 / Net I/av σ(I): 7.048 / Net I/σ(I): 25.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.2→132.1 Å / Cor.coef. Fo:Fc: 0.877 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.572 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 max: 173.15 Å2 / Biso mean: 93.591 Å2 / Biso min: 49.44 Å2
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Refinement step | Cycle: final / Resolution: 3.2→132.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.2→3.283 Å / Total num. of bins used: 20
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