+Open data
-Basic information
Entry | Database: PDB / ID: 3r0l | |||||||||
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Title | Crystal structure of crotoxin | |||||||||
Components |
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Keywords | TOXIN/HYDROLASE / crotoxin / presynaptic neurotoxin / snake venom / phospholipase A2 / heterodimer interface / hydrolase / lipid degradation / metal-binding / TOXIN-HYDROLASE complex | |||||||||
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: 1.35 Å | |||||||||
Authors | Saul, F.A. / Faure, G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Crystal Structure of Crotoxin Reveals Key Residues Involved in the Stability and Toxicity of This Potent Heterodimeric Beta-Neurotoxin Authors: Faure, G. / Xu, H. / Saul, F.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3r0l.cif.gz | 61.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3r0l.ent.gz | 43 KB | Display | PDB format |
PDBx/mmJSON format | 3r0l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3r0l_validation.pdf.gz | 466.4 KB | Display | wwPDB validaton report |
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Full document | 3r0l_full_validation.pdf.gz | 467.3 KB | Display | |
Data in XML | 3r0l_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | 3r0l_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/3r0l ftp://data.pdbj.org/pub/pdb/validation_reports/r0/3r0l | HTTPS FTP |
-Related structure data
Related structure data | 2qogS 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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Unit cell |
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Details | THE BIOLOGICAL UNIT IS A HETERODIMER FORMED BY THE NON-COVALENT ASSOCIATION OF THE CROTOXIN ACID SUBUNIT (CHAINS A, B, C) WITH THE BASIC SUBUNIT (CHAIN D). |
-Components
-Crotoxin chain ... , 3 types, 3 molecules ABC
#1: Protein/peptide | Mass: 4159.536 Da / Num. of mol.: 1 / Fragment: Crotoxin acidic subunit isoform CA2 alpha chain / Source method: isolated from a natural source / Details: from South American rattlesnake venom Source: (natural) Crotalus durissus terrificus (tropical rattlesnake) References: UniProt: P08878 |
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#2: Protein/peptide | Mass: 3753.091 Da / Num. of mol.: 1 / Fragment: Crotoxin acidic subunit isoform CA2 beta chain / Source method: isolated from a natural source / Details: from South American rattlesnake venom Source: (natural) Crotalus durissus terrificus (tropical rattlesnake) References: UniProt: P08878 |
#3: Protein/peptide | Mass: 1536.599 Da / Num. of mol.: 1 / Fragment: Crotoxin acidic subunit isoform CA2 gamma chain / Source method: isolated from a natural source / Details: from South American rattlesnake venom Source: (natural) Crotalus durissus terrificus (tropical rattlesnake) References: UniProt: P08878 |
-Protein , 1 types, 1 molecules D
#4: Protein | Mass: 14188.321 Da / Num. of mol.: 1 / Fragment: Crotoxin basic subunit CB / Source method: isolated from a natural source / Details: from South American rattlesnake venom Source: (natural) Crotalus durissus terrificus (tropical rattlesnake) References: UniProt: P62022, UniProt: P0CG56*PLUS, phospholipase A2 |
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-Non-polymers , 5 types, 270 molecules
#5: Chemical | ChemComp-CL / | ||||
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#6: Chemical | ChemComp-MN / | ||||
#7: Chemical | #8: Chemical | ChemComp-ACT / | #9: Water | ChemComp-HOH / | |
-Details
Sequence details | IN CHAINS B AND C, THE N-TERMINI ARE MODIFIED WITH A PCA IN PLACE OF GLN. CHAIN A ISOFORM CA2 ...IN CHAINS B AND C, THE N-TERMINI ARE MODIFIED WITH A PCA IN PLACE OF GLN. CHAIN A ISOFORM CA2 CONTAINS 39 AMINO ACID RESIDUES (FAURE ET AL. (1991) BIOCHEMIST |
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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: 1.73 Å3/Da / Density % sol: 28.9 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 30% PEG 4000, 0.1 M sodium acetate, 0.1 M magnesium chloride, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.918 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2009 |
Radiation | Monochromator: Si (111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→36.33 Å / Num. obs: 35132 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 12.98 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 1.9 / % possible all: 96.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QOG Resolution: 1.35→36.33 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.088 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.06 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→36.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.37 Å / Total num. of bins used: 40
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