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Yorodumi- PDB-4i8y: Structure of the unliganded N254Y/H258Y mutant of the phosphatidy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i8y | ||||||
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Title | Structure of the unliganded N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from S. aureus | ||||||
Components | 1-phosphatidylinositol phosphodiesterase | ||||||
Keywords | hydrolase / lyase / TIM barrel / phospholipase | ||||||
Function / homology | Function and homology information phosphatidylinositol diacylglycerol-lyase / phosphatidylinositol diacylglycerol-lyase activity / phosphoric diester hydrolase activity / lipid catabolic process / extracellular region Similarity search - Function | ||||||
Biological species | Staphylococcus aureus subsp. aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Goldstein, R.I. / Cheng, J. / Stec, B. / Gershenson, A. / Roberts, M.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2013 Title: The cation-pi box is a specific phosphatidylcholine membrane targeting motif. Authors: Cheng, J. / Goldstein, R. / Gershenson, A. / Stec, B. / Roberts, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4i8y.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i8y.ent.gz | 56.7 KB | Display | PDB format |
PDBx/mmJSON format | 4i8y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i8/4i8y ftp://data.pdbj.org/pub/pdb/validation_reports/i8/4i8y | HTTPS FTP |
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-Related structure data
Related structure data | 4i90C 4i9jC 4i9mC 4i9tC 3v18S 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34487.367 Da / Num. of mol.: 1 / Mutation: N254Y, H258Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus subsp. aureus (bacteria) Strain: Newman / Gene: plc, NWMN_0041 / Production host: Escherichia coli (E. coli) References: UniProt: P45723, phosphatidylinositol diacylglycerol-lyase |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-ACT / |
#4: 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: 2.2 Å3/Da / Density % sol: 44.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 26% PEG 4000, 0.1M magnesium nitrate, 0.15M ammonium acetate, 0.1M sodium acetate, 0.1M myo-inositol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 7, 2011 / Details: Osmic VariMax |
Radiation | Monochromator: Osmic Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. all: 98275 / Num. obs: 98275 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 29.521 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2.936 / Num. unique all: 838 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3V18 Resolution: 2.1→49.87 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.933 / SU B: 0.007 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.153 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.143 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→49.87 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.099→2.153 Å / Total num. of bins used: 20
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