+Open data
-Basic information
Entry | Database: PDB / ID: 2qog | ||||||
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Title | Crotoxin B, the basic PLA2 from Crotalus durissus terrificus. | ||||||
Components |
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Keywords | HYDROLASE / Crotoxin B CD-Cdt Basic-PLA2 / Calcium / Lipid degradation / Metal-binding / Secreted / Neurotoxin / Presynaptic neurotoxin | ||||||
Function / homology | Function and homology information envenomation resulting in induction of edema in another organism / envenomation resulting in muscle damage in another organism / envenomation resulting in myocyte killing in another organism / envenomation resulting in positive regulation of platelet aggregation in another organism / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / ion channel regulator activity / calcium-dependent phospholipase A2 activity / phospholipase A2 ...envenomation resulting in induction of edema in another organism / envenomation resulting in muscle damage in another organism / envenomation resulting in myocyte killing in another organism / envenomation resulting in positive regulation of platelet aggregation in another organism / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / ion channel regulator activity / calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / phospholipid binding / toxin activity / calcium ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Crotalus durissus terrificus (tropical rattlesnake) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.28 Å | ||||||
Authors | Marchi-Salvador, D.P. / Correa, L.C. / Fontes, M.R.M. | ||||||
Citation | Journal: Proteins / Year: 2008 Title: Insights into the role of oligomeric state on the biological activities of crotoxin: crystal structure of a tetrameric phospholipase A2 formed by two isoforms of crotoxin B from Crotalus durissus terrificus venom. Authors: Marchi-Salvador, D.P. / Correa, L.C. / Magro, A.J. / Oliveira, C.Z. / Soares, A.M. / Fontes, M.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2qog.cif.gz | 111.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2qog.ent.gz | 92.5 KB | Display | PDB format |
PDBx/mmJSON format | 2qog.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qo/2qog ftp://data.pdbj.org/pub/pdb/validation_reports/qo/2qog | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is a tetramer generated from the tetramer (two dimers) in the asymmetric unit. |
-Components
#1: Protein | Mass: 14281.440 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Venom glands Source: (natural) Crotalus durissus terrificus (tropical rattlesnake) Species: Crotalus durissus / Strain: terrificus / References: UniProt: P24027, phospholipase A2 #2: Protein | Mass: 14220.405 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Venom glands Source: (natural) Crotalus durissus terrificus (tropical rattlesnake) Species: Crotalus durissus / Strain: terrificus / References: UniProt: P62022, phospholipase A2 #3: Chemical | #4: 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: 2.6 Å3/Da / Density % sol: 52.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M Tris HCl and 11% (w/v) PEG 8000, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.427 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 14, 2006 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.427 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→40 Å / Num. obs: 27552 / % possible obs: 85.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 9.57 |
Reflection shell | Resolution: 2.28→2.36 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.547 / Mean I/σ(I) obs: 2.04 / Num. unique all: 2423 / Rsym value: 0.547 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: monomer A of BthTX-I (closed form) Resolution: 2.28→28.93 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1059991.12 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.8119 Å2 / ksol: 0.320295 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→28.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.42 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
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Xplor file |
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