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Yorodumi- PDB-1t7e: Crystal structure of mutant Pro9Ser of scorpion alpha-like neurot... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1t7e | ||||||
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Title | Crystal structure of mutant Pro9Ser of scorpion alpha-like neurotoxin BmK M1 from Buthus martensii Karsch | ||||||
Components | Alpha-like neurotoxin BmK-I | ||||||
Keywords | TOXIN / BmK M1 mutant / Scorpion toxin / Buthus martensii Karsch | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Xiang, Y. / Guan, R.J. / He, X.L. / Wang, C.G. / Wang, M. / Zhang, Y. / Sundberg, E.J. / Wang, D.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: Structural Mechanism Governing Cis and Trans Isomeric States and an Intramolecular Switch for Cis/Trans Isomerization of a Non-proline Peptide Bond Observed in Crystal Structures of Scorpion Toxins Authors: Guan, R.J. / Xiang, Y. / He, X.L. / Wang, C.G. / Wang, M. / Zhang, Y. / Sundberg, E.J. / Wang, D.C. #1: 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. #2: Journal: Protein Expr.Purif. / Year: 1999 Title: Expression and purification of the BmK M1 neurotoxin from the scorpion Buthus martensii Karsch Authors: Shao, F. / Xiong, Y.M. / Zhu, R.H. / Ling, M.H. / Chi, C.W. / Wang, D.C. #3: Journal: Toxicon / Year: 1997 Title: The CDNA and genomic DNA sequences of a mammalian neurotoxin from the scorpion Buthus martensii Karsch Authors: Xiong, Y.M. / Ling, M.H. / Wang, D.C. / Chi, C.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1t7e.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1t7e.ent.gz | 18 KB | Display | PDB format |
PDBx/mmJSON format | 1t7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/1t7e ftp://data.pdbj.org/pub/pdb/validation_reports/t7/1t7e | HTTPS FTP |
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-Related structure data
Related structure data | 1kv0C 1t7aC 1t7bC 1sn1S S: Starting model for refinement C: citing same article (ref.) |
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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: 7426.419 Da / Num. of mol.: 1 / Mutation: P9S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mesobuthus martensii (Chinese scorpion) Gene: BmK M1 / Plasmid: PVT 102U-ALPHA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): S-78 / References: UniProt: P45697 | ||
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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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: Sodium phosphate, PEG400, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 283 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 20, 2000 |
Radiation | Monochromator: SILICON (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→30 Å / Num. all: 13889 / Num. obs: 13889 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 20.4 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.355 / Mean I/σ(I) obs: 2 / Num. unique all: 1988 / Rsym value: 0.355 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SN1 Resolution: 1.4→19 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.464 / SU ML: 0.059 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.068 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 15.27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→19 Å
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Refine LS restraints |
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LS refinement shell | Highest resolution: 1.4 Å / Num. reflection Rwork: 1178 / Total num. of bins used: 15 |