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Yorodumi- PDB-4f2b: Modulation of S.Aureus Phosphatidylinositol-Specific Phospholipas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f2b | ||||||
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Title | Modulation of S.Aureus Phosphatidylinositol-Specific Phospholipase C Membrane Binding | ||||||
Components | 1-phosphatidylinositol phosphodiesterase | ||||||
Keywords | LYASE / Dimer / Phosphatidylinositol-specific Phospholipase C | ||||||
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: 2.16 Å | ||||||
Authors | Cheng, J. / Goldstein, R. / Stec, B. / Gershenson, A. / Roberts, M.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Competition between Anion Binding and Dimerization Modulates Staphylococcus aureus Phosphatidylinositol-specific Phospholipase C Enzymatic Activity. Authors: Cheng, J. / Goldstein, R. / Stec, B. / Gershenson, A. / 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 | 4f2b.cif.gz | 131.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f2b.ent.gz | 103.1 KB | Display | PDB format |
PDBx/mmJSON format | 4f2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/4f2b ftp://data.pdbj.org/pub/pdb/validation_reports/f2/4f2b | HTTPS FTP |
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-Related structure data
Related structure data | 4f2tC 4f2uC 3v16S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35242.141 Da / Num. of mol.: 2 / Fragment: UNP residues 11-312 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 #2: Chemical | #3: 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: 2.06 Å3/Da / Density % sol: 40.27 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20% PEG 4000, 0.150 M ammonium acetate, 0.100 M sodium acetate, 0.001 M magnesium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 120 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: Dec 19, 2011 / Details: Osmic VariMax | |||||||||||||||
Radiation | Monochromator: RIGAKU MICROMAX-07 HF MICROFOCUS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.16→50 Å / Num. all: 116278 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.092 | |||||||||||||||
Reflection shell | Resolution: 2.16→2.22 Å / Redundancy: 3.9 % / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3V16 Resolution: 2.16→50 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.296 / SU ML: 0.257 / Cross valid method: THROUGHOUT / σ(F): 2.2 / ESU R: 0.043 / ESU R Free: 0.05 / 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: 42.531 Å2
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Refinement step | Cycle: LAST / Resolution: 2.16→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.16→2.218 Å / Total num. of bins used: 20
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