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Yorodumi- PDB-4f2t: Modulation of S.aureus Phosphatidylinositol-Specific Phospholipas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4f2t | ||||||
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Title | Modulation of S.aureus Phosphatidylinositol-Specific Phospholipase C Membrane Binding. | ||||||
Components | 1-phosphatidylinositol phosphodiesterase | ||||||
Keywords | LYASE / alpha beta barrel / phosphatidylinostol-specific phospholipase C / membrane interface | ||||||
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: 2.3 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 | 4f2t.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f2t.ent.gz | 55.3 KB | Display | PDB format |
PDBx/mmJSON format | 4f2t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f2t_validation.pdf.gz | 438.6 KB | Display | wwPDB validaton report |
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Full document | 4f2t_full_validation.pdf.gz | 441.6 KB | Display | |
Data in XML | 4f2t_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 4f2t_validation.cif.gz | 18.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f2/4f2t ftp://data.pdbj.org/pub/pdb/validation_reports/f2/4f2t | HTTPS FTP |
-Related structure data
Related structure data | 4f2bC 4f2uC 3v18S 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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Unit cell |
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-Components
#1: Protein | Mass: 35166.047 Da / Num. of mol.: 1 / Fragment: UNP residues 11-312 / Mutation: Y253S 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 | #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: 2.11 Å3/Da / Density % sol: 41.77 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 16% PEG 4000, 0.150 M ammonium acetate, 0.100 M sodium acetate, 0.100 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: Jan 24, 2012 / 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→50 Å / Num. all: 274181 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.3 % / Rmerge(I) obs: 0.063 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 12.3 % / Num. unique all: 997 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3V18 Resolution: 2.3→29.855 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 22.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.729 Å2 / ksol: 0.306 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.3→29.855 Å
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Refine LS restraints |
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LS refinement shell |
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