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Yorodumi- PDB-4rw5: Structural insights into substrate binding of brown spider venom ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rw5 | ||||||
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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: 1.64 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4rw5.cif.gz | 68.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rw5.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 4rw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rw5_validation.pdf.gz | 778.5 KB | Display | wwPDB validaton report |
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Full document | 4rw5_full_validation.pdf.gz | 783.5 KB | Display | |
Data in XML | 4rw5_validation.xml.gz | 14.2 KB | Display | |
Data in CIF | 4rw5_validation.cif.gz | 19.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rw/4rw5 ftp://data.pdbj.org/pub/pdb/validation_reports/rw/4rw5 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33672.625 Da / Num. of mol.: 1 / Mutation: H12A 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 |
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-Non-polymers , 6 types, 89 molecules
#2: Chemical | ChemComp-MG / |
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#3: Chemical | ChemComp-PLM / |
#4: Chemical | ChemComp-GOL / |
#5: Chemical | ChemComp-TDA / |
#6: Chemical | ChemComp-OCA / |
#7: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.59 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Tris-HCl pH 7.5, 40% PEG 200, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD |
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: 1.6→24.49 Å / Num. all: 47089 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→24.49 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.097 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 24.91 Å2
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Refinement step | Cycle: LAST / Resolution: 1.64→24.49 Å
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Refine LS restraints |
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