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Yorodumi- PDB-4i9m: Structure of the N254Y/H258Y mutant of the phosphatidylinositol-s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4i9m | ||||||
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Title | Structure of the N254Y/H258Y mutant of the phosphatidylinositol-specific phospholipase C from Staphylococcus aureus bound to HEPES | ||||||
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: 2.2 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 | 4i9m.cif.gz | 81.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4i9m.ent.gz | 59.4 KB | Display | PDB format |
PDBx/mmJSON format | 4i9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4i9m_validation.pdf.gz | 444.2 KB | Display | wwPDB validaton report |
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Full document | 4i9m_full_validation.pdf.gz | 447.7 KB | Display | |
Data in XML | 4i9m_validation.xml.gz | 16.7 KB | Display | |
Data in CIF | 4i9m_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i9/4i9m ftp://data.pdbj.org/pub/pdb/validation_reports/i9/4i9m | HTTPS FTP |
-Related structure data
Related structure data | 4i8yC 4i90C 4i9jC 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: 35316.238 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 | ChemComp-SO4 / | #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: 2.11 Å3/Da / Density % sol: 41.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 22% PEG 4000, 0.1M HEPES,10% isopropanol, pH 7.5, 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: Aug 15, 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: 2.2→50 Å / Num. all: 94114 / Num. obs: 94114 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.117 / Rsym value: 0.117 / Net I/σ(I): 26.494 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6 % / Rmerge(I) obs: 0.665 / Mean I/σ(I) obs: 3.75 / Num. unique all: 769 / Rsym value: 0.665 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3V18 Resolution: 2.2→30.854 Å / SU ML: 0.3 / σ(F): 1.34 / Phase error: 20.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.447 Å2 / ksol: 0.3 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.2→30.854 Å
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Refine LS restraints |
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LS refinement shell |
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