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Yorodumi- PDB-6tmy: Crystal structure of isoform CBd of the basic phospholipase A2 su... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tmy | ||||||
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Title | Crystal structure of isoform CBd of the basic phospholipase A2 subunit of crotoxin from Crotalus durissus terrificus | ||||||
Components | Phospholipase A2 crotoxin basic subunit CBc | ||||||
Keywords | HYDROLASE / crotoxin / CB isoforms / presynaptic phospholipase A2 | ||||||
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 / ion channel regulator activity / phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate secretion / phospholipid metabolic process / lipid catabolic process ...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 / ion channel regulator activity / phospholipase A2 / calcium-dependent phospholipase A2 activity / arachidonate 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: 1.8 Å | ||||||
Authors | Nemecz, D. / Ostrowski, M. / Saul, F.A. / Faure, G. | ||||||
Funding support | Poland, 1items
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Citation | Journal: Molecules / Year: 2020 Title: Crystal Structure of Isoform CBd of the Basic Phospholipase A 2 Subunit of Crotoxin: Description of the Structural Framework of CB for Interaction with Protein Targets. Authors: Nemecz, D. / Ostrowski, M. / Ravatin, M. / Saul, F. / Faure, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tmy.cif.gz | 185.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tmy.ent.gz | 146.9 KB | Display | PDB format |
PDBx/mmJSON format | 6tmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tmy_validation.pdf.gz | 477.2 KB | Display | wwPDB validaton report |
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Full document | 6tmy_full_validation.pdf.gz | 482.6 KB | Display | |
Data in XML | 6tmy_validation.xml.gz | 38.5 KB | Display | |
Data in CIF | 6tmy_validation.cif.gz | 55.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tm/6tmy ftp://data.pdbj.org/pub/pdb/validation_reports/tm/6tmy | HTTPS FTP |
-Related structure data
Related structure data | 3r0lS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14280.483 Da / Num. of mol.: 6 / Source method: isolated from a natural source Source: (natural) Crotalus durissus terrificus (tropical rattlesnake) References: UniProt: P62022, phospholipase A2 #2: Chemical | ChemComp-NA / #3: Chemical | ChemComp-PG4 / #4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | Has protein modification | Y | |
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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: 3.06 Å3/Da / Density % sol: 59.75 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400, 0.1M NACL, 0.18M SODIUM ACETATE, 0.1M TRIS |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 25, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.5 Å / Num. obs: 94489 / % possible obs: 98.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 33.29 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.8→1.83 Å / Redundancy: 4 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 4708 / % possible all: 97 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3R0L POLYPEPTIDE CHAIN D Resolution: 1.8→47.5 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.938 / SU R Cruickshank DPI: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.118 / SU Rfree Blow DPI: 0.108 / SU Rfree Cruickshank DPI: 0.103
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Displacement parameters | Biso max: 125.64 Å2 / Biso mean: 37.38 Å2 / Biso min: 16.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.25 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→47.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
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