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Yorodumi- PDB-4i90: Structure of the N254Y/H258Y mutant of the phosphatidylinositol-s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i90 | ||||||
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Title | Structure of the N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from S. aureus bound to choline | ||||||
Components | 1-phosphatidylinositol phosphodiesterase | ||||||
Keywords | hydrolase / lyase / TIM barrel / phospholipase / choline binding | ||||||
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: 1.65 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 | 4i90.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i90.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 4i90.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i90_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 4i90_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 4i90_validation.xml.gz | 16 KB | Display | |
Data in CIF | 4i90_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/4i90 ftp://data.pdbj.org/pub/pdb/validation_reports/i9/4i90 | HTTPS FTP |
-Related structure data
Related structure data | 4i8yC 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: 34358.254 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 | #3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.22 Å3/Da / Density % sol: 44.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25% PEG 4000, 0.1M sodium acetate, 0.1M magnesium acetate, 0.150M ammonium acetate, 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, 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: 1.65→50 Å / Num. all: 341705 / Num. obs: 341705 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 72.067 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.651 / Mean I/σ(I) obs: 2.78 / Num. unique all: 1344 / Rsym value: 0.651 / % possible all: 73.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3V18 Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.948 / SU B: 0.005 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.11 / 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: 29.176 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.649→1.692 Å / Total num. of bins used: 20
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