+Open data
-Basic information
Entry | Database: PDB / ID: 1npi | ||||||
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Title | Tityus Serrulatus Neurotoxin (Ts1) at atomic resolution | ||||||
Components | Toxin VII | ||||||
Keywords | TOXIN / XCITATORY 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: 1.16 Å | ||||||
Authors | Pinheiro, C.B. / Marangoni, S. / Toyama, M.H. / Polikarpov, I. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Structural analysis of Tityus serrulatus Ts1 neurotoxin at atomic resolution: insights into interactions with Na+ channels. Authors: Pinheiro, C.B. / Marangoni, S. / Toyama, M.H. / Polikarpov, I. #1: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Crystallization and preliminary diffraction data of neurotoxin Ts-c from the venom of the scorpion Tityus serrulatus Authors: Golubev, A.M. / Lee, W.H. / Marangoni, S. / Novello, J.C. / Oliveira, B. / Toyama, M.H. / Polikarpov, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1npi.cif.gz | 44.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1npi.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 1npi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1npi_validation.pdf.gz | 421.8 KB | Display | wwPDB validaton report |
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Full document | 1npi_full_validation.pdf.gz | 421.7 KB | Display | |
Data in XML | 1npi_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | 1npi_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/1npi ftp://data.pdbj.org/pub/pdb/validation_reports/np/1npi | HTTPS FTP |
-Related structure data
Related structure data | 1b7dS 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) / References: UniProt: P15226 | ||
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#2: Chemical | #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: 1.54 Å3/Da / Density % sol: 13.83 % | ||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, potassium phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||
Crystal grow | *PLUS Details: Golubev, A.M., (1998) Acta Crystallogr., Sect.D, 54, 1440.PH range low: 6.5 / PH range high: 5.2 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.28, 1.38 | |||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1999 | |||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.16→12.5 Å / Num. all: 16095 / Num. obs: 11943 / % possible obs: 92 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 3 % / Rsym value: 0.078 / Net I/σ(I): 12 | |||||||||
Reflection shell | Resolution: 1.16→1.19 Å / % possible all: 52 | |||||||||
Reflection | *PLUS Lowest resolution: 12 Å / % possible obs: 92 % / Num. measured all: 16095 / Rmerge(I) obs: 0.078 | |||||||||
Reflection shell | *PLUS % possible obs: 52 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1B7D Resolution: 1.16→12.5 Å / Num. parameters: 5797 / Num. restraintsaints: 5711 / Cross valid method: FREE R / σ(F): 4 / σ(I): 2
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Refine analyze | Num. disordered residues: 7 / Occupancy sum hydrogen: 442.78 / Occupancy sum non hydrogen: 574.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→12.5 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL / Version: 97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.1587 / Rfactor Rwork: 0.0974 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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