[English] 日本語
Yorodumi- PDB-4rv3: Crystal structure of a pentafluoro-Phe incorporated Phosphatidyli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rv3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a pentafluoro-Phe incorporated Phosphatidylinositol-specific phospholipase C (H258X)from Staphylococcus aureus | ||||||
Components | 1-phosphatidylinositol phosphodiesterase | ||||||
Keywords | LYASE / cation-pi / TIM barrel / encoded unnatural amino acid 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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | He, T. / Gershenson, A. / Eyles, S.J. / Gao, J. / Roberts, M.F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2015 Title: Fluorinated Aromatic Amino Acids Distinguish Cation-pi Interactions from Membrane Insertion. Authors: He, T. / Gershenson, A. / Eyles, S.J. / Lee, Y.J. / Liu, W.R. / Wang, J. / Gao, J. / Roberts, M.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rv3.cif.gz | 72.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rv3.ent.gz | 57.3 KB | Display | PDB format |
PDBx/mmJSON format | 4rv3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rv/4rv3 ftp://data.pdbj.org/pub/pdb/validation_reports/rv/4rv3 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34296.055 Da / Num. of mol.: 1 / Mutation: H258(PF5) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P45723, phosphatidylinositol diacylglycerol-lyase |
---|---|
#2: Chemical | ChemComp-ACT / |
#3: Chemical | ChemComp-INS / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 26% PEG 4000,0.150M ammonium acetate,0.1M sodium acetate, 0.1M magnesium nitrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 28, 2014 |
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→49.87 Å / Num. all: 23089 / Num. obs: 22311 / % possible obs: 96.61 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.31 % |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 2.13 % / Rmerge(I) obs: 0.199 / Mean I/σ(I) obs: 3.9 / % possible all: 74.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→49.87 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 23.12 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→49.87 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|