[English] 日本語
Yorodumi- PDB-4rw3: Structural insights into substrate binding of brown spider venom ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rw3 | ||||||
---|---|---|---|---|---|---|---|
Title | Structural insights into substrate binding of brown spider venom class II phospholipases D | ||||||
Components | Phospholipase D LiSicTox-alphaIA1bii | ||||||
Keywords | HYDROLASE / TIM-barrel fold | ||||||
Function / homology | Function and homology information phosphoric diester hydrolase activity / lipid catabolic process / Lyases; Phosphorus-oxygen lyases / toxin activity / killing of cells of another organism / lyase activity / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | Loxosceles intermedia (spider) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Coronado, M.A. / Ullah, A. / da Silva, L.S. / Chaves-Moreira, D. / Vuitika, L. / Chaim, O.M. / Veiga, S.S. / Chahine, J. / Murakami, M.T. / Arni, R.K. | ||||||
Citation | Journal: Curr Protein Pept Sci / Year: 2015 Title: Structural Insights into Substrate Binding of Brown Spider Venom Class II Phospholipases D. Authors: Coronado, M.A. / Ullah, A. / da Silva, L.S. / Chaves-Moreira, D. / Vuitika, L. / Chaim, O.M. / Veiga, S.S. / Chahine, J. / Murakami, M.T. / Arni, R.K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4rw3.cif.gz | 81.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4rw3.ent.gz | 57.2 KB | Display | PDB format |
PDBx/mmJSON format | 4rw3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rw3_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4rw3_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 4rw3_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 4rw3_validation.cif.gz | 23.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/4rw3 ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rw3 | HTTPS FTP |
-Related structure data
Related structure data | 4rw5C 3rlhS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33739.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Loxosceles intermedia (spider) / Production host: Escherichia coli (E. coli) / References: UniProt: P0CE82, phospholipase D |
---|
-Non-polymers , 10 types, 181 molecules
#2: Chemical | ChemComp-MG / | ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-IPD / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-OCA / | #7: Chemical | ChemComp-SHV / | #8: Chemical | #9: Chemical | #10: Chemical | ChemComp-TDA / | #11: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.6 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris-HCl pH 7.5, 40% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 291K PH range: 7,5 |
-Data collection
Diffraction | Mean temperature: 200 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 20, 2014 |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.458 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→30 Å / Num. all: 28074 / Num. obs: 25218 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 3RLH Resolution: 1.72→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.898 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.529 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|