+Open data
-Basic information
Entry | Database: PDB / ID: 1sn1 | ||||||
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Title | STRUCTURE OF SCORPION NEUROTOXIN BMK M1 | ||||||
Components | PROTEIN (NEUROTOXIN BMK M1) | ||||||
Keywords | TOXIN / NEUROTOXIN / SODIUM CHANNEL INHIBITOR / SCORPION | ||||||
Function / homology | Function and homology information sodium channel inhibitor activity / defense response / toxin activity / extracellular region Similarity search - Function | ||||||
Biological species | Mesobuthus martensii (Chinese scorpion) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | He, X.L. / Li, H.M. / Liu, X.Q. / Zeng, Z.H. / Wang, D.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Crystal structures of two alpha-like scorpion toxins: non-proline cis peptide bonds and implications for new binding site selectivity on the sodium channel. Authors: He, X.L. / Li, H.M. / Zeng, Z.H. / Liu, X.Q. / Wang, M. / Wang, D.C. #1: Journal: J.Mol.Biol. / Year: 1996 Title: Crystal Structure of an Acidic Neurotoxin from Scorpion Buthus Martensii Karsch at 1.85 A Resolution Authors: Li, H.M. / Wang, D.C. / Zeng, Z.H. / Jin, L. / Hu, R.Q. #2: Journal: Toxicon / Year: 1996 Title: Two Neurotoxins (Bmk I and Bmk II) from the Venom of the Scorpion Buthus Martensii Karsch-Purification, Amino Acid Sequence and Assessment of Specific Activity Authors: Ji, Y.H. / Mansuelle, P. / Terakawa, S. / Kopeyan, C. #3: Journal: J.Mol.Biol. / Year: 1994 Title: Crystal Structure of Toxin II from the Scorpion Androctonus Australis Hector Refined at 1.3 A Resolution Authors: Housset, D. / Habersetzer-Rochat, C. / Astier, J.P. / Fontecilla-Camps, J.C. #4: Journal: J.Mol.Biol. / Year: 1992 Title: Structure of Scorpion Toxin Variant-3 at 1.2 A Resolution Authors: Zhao, B. / Carson, M. / Ealick, S.E. / Bugg, C.E. #5: Journal: Dongwuxue Yanjiu / Year: 1989 Title: Purification and Partial Characterization of Several New Neurotoxins from East- Asia Scorpion [Chinese] Authors: Hu, R.Q. / Wang, M. / Liu, J.N. / Lei, K.J. #6: Journal: J.Mol.Biol. / Year: 1983 Title: Structure of Variant-3 Scorpion Neurotoxin from Centruroides Sculpturatus Ewing, Refined at 1.8 A Resolution Authors: Almassy, R.J. / Fontecilla-Camps, J.C. / Suddath, F.L. / Bugg, C.E. #7: Journal: Proc.Natl.Acad.Sci.USA / Year: 1980 Title: Three-Dimensional Structure of a Protein from Scorpion Venom. A New Structural Class of Neurotoxins Authors: Fontecilla-Camps, J.C. / Almassy, R.J. / Suddath, F.L. / Watt, D.D. / Bugg, C.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1sn1.cif.gz | 27.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1sn1.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 1sn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sn1_validation.pdf.gz | 363 KB | Display | wwPDB validaton report |
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Full document | 1sn1_full_validation.pdf.gz | 364.4 KB | Display | |
Data in XML | 1sn1_validation.xml.gz | 2.9 KB | Display | |
Data in CIF | 1sn1_validation.cif.gz | 4.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/1sn1 ftp://data.pdbj.org/pub/pdb/validation_reports/sn/1sn1 | HTTPS FTP |
-Related 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: 7235.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Organ: TAIL / Secretion: VENOM / References: UniProt: P45697 |
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#2: 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: 2.88 Å3/Da / Density % sol: 57.3 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 57.3 % | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 23 ℃ / Method: batch method | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.5418 |
Detector | Type: SIEMENS X200B / Detector: AREA DETECTOR / Date: Dec 14, 1991 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→29.3 Å / Num. obs: 8360 / % possible obs: 87.3 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.7→1.8 Å / % possible all: 60.2 |
Reflection | *PLUS Num. measured all: 20330 / Rmerge(I) obs: 0.05 |
Reflection shell | *PLUS % possible obs: 52.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: BMK M8 Resolution: 1.7→100 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 1.0E-5 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 34.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.72→1.78 Å / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.169 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 34.9 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.336 / % reflection Rfree: 10 % / Rfactor Rwork: 0.269 |