+Open data
-Basic information
Entry | Database: PDB / ID: 1b7d | ||||||
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Title | NEUROTOXIN (TS1) FROM BRAZILIAN SCORPION TITYUS SERRULATUS | ||||||
Components | PROTEIN (NEUROTOXIN TS1) | ||||||
Keywords | TOXIN / LONG-CHAIN NEUROTOXIN | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / defense response to fungus / toxin activity / killing of cells of another organism / extracellular region Similarity search - Function | ||||||
Biological species | Tityus serrulatus (Brazilian scorpion) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å | ||||||
Authors | Polikarpov, I. / Sanches Jr., M.S. / Marangoni, S. / Toyama, M.H. / Teplyakov, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structure of neurotoxin Ts1 from Tityus serrulatus provides insights into the specificity and toxicity of scorpion toxins. Authors: Polikarpov, I. / Junior, M.S. / Marangoni, S. / Toyama, M.H. / Teplyakov, A. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallisation and Preliminary Diffraction Data of Neurotoxin Ts-Gamma from the Venom of Scorpion Tityus Serrulatus Authors: Golubev, A.M. / Lee, W.H. / Marangoni, S. / Novello, J.C. / Oliveira, B. / Toyama, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b7d.cif.gz | 26.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b7d.ent.gz | 15.9 KB | Display | PDB format |
PDBx/mmJSON format | 1b7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b7/1b7d ftp://data.pdbj.org/pub/pdb/validation_reports/b7/1b7d | HTTPS FTP |
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-Related structure data
Related structure data | 1ahoS 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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-Components
#1: Protein | Mass: 6901.012 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Tityus serrulatus (Brazilian scorpion) / Secretion: VENOM / References: UniProt: P15226 |
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#2: Chemical | ChemComp-PO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 32.84 % Description: DIFFRACTION DATA HAVE BEEN COLLECTED AT THE LABORATORIO NACIONAL DE LUZ SINCROTRON (LNLS), CAMPINAS, BRAZIL | ||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.0 | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging dropDetails: 0.01ml protein solution was mixed with 0.005ml reservoir PH range low: 6.5 / PH range high: 5.2 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.37 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: CYLINDRICAL MIRROR |
Radiation | Monochromator: SI BENT SINGLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.37 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→13 Å / Num. obs: 5149 / % possible obs: 97.1 % / Redundancy: 2.6 % / Rsym value: 0.066 |
Reflection shell | Resolution: 1.73→1.77 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3 / Rsym value: 0.26 / % possible all: 81.6 |
Reflection | *PLUS Num. measured all: 13402 / Rmerge(I) obs: 0.066 |
Reflection shell | *PLUS % possible obs: 81.6 % / Rmerge(I) obs: 0.26 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1AHO Resolution: 1.73→13 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 21.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.73→13 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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