+Open data
-Basic information
Entry | Database: PDB / ID: 3bjw | |||||||||
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Title | Crystal Structure of ecarpholin S complexed with suramin | |||||||||
Components | Phospholipase A2 | |||||||||
Keywords | HYDROLASE / snake venom / Phospholipase A2 / suramin / Ser49 / complex / Calcium / Lipid degradation / Metal-binding / Secreted / Toxin | |||||||||
Function / homology | Function and homology information calcium-dependent phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / calcium ion binding / extracellular region Similarity search - Function | |||||||||
Biological species | Echis carinatus (saw-scaled viper) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | |||||||||
Authors | Zhou, X. / Sivaraman, J. | |||||||||
Citation | Journal: Biophys.J. / Year: 2008 Title: Structural Characterization of Myotoxic Ecarpholin S from Echis carinatus Venom Authors: Zhou, X. / Tan, T.C. / Valiyaveettil, S. / Go, M.L. / Kini, R.M. / Velazquez-Campoy, A. / Sivaraman, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bjw.cif.gz | 229.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bjw.ent.gz | 193.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bjw ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bjw | HTTPS FTP |
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-Related structure data
Related structure data | 2qhdC 2qheC 1jiaS S: Starting model for refinement C: citing same article (ref.) |
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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: 13838.879 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Echis carinatus (saw-scaled viper) / References: UniProt: P48650, phospholipase A2 #2: Chemical | ChemComp-SVR / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.89 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 5.6 Details: 10% PEG3350, 10% iso-propanol, 0.1M sodium citrate, the ratio of suramin to protein is 1.5:1, pH5.6, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 12, 2006 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 55923 / % possible obs: 97.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.089 / Χ2: 0.998 / Net I/σ(I): 8.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.386 / Num. unique all: 4937 / Χ2: 0.918 / % possible all: 86.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JIA Resolution: 2.3→20 Å / FOM work R set: 0.796 / σ(F): 4322
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Solvent computation | Bsol: 32.932 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.702 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms: 0 / Type: restrain / Weight: 300 | ||||||||||||||||||||||||||||
Xplor file |
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