+Open data
-Basic information
Entry | Database: PDB / ID: 1chz | ||||||
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Title | A NEW NEUROTOXIN FROM BUTHUS MARTENSII KARSCH | ||||||
Components | PROTEIN (BMK M2) | ||||||
Keywords | TOXIN / NEUROTOXIN / 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: 1.76 Å | ||||||
Authors | He, X.L. / Deng, J.P. / Li, H.M. / Wang, D.C. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Structure of a new neurotoxin from the scorpion Buthus martensii Karsch at 1.76 A. Authors: He, X.L. / Deng, J.P. / Wang, M. / Zhang, Y. / 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: Zool.Res.Sinica. / Year: 1989 Title: Purification and Partial Characterization of Several New Nerotoxins from East- Asia Scorpion Authors: Hu, R.Q. / Wang, M. / Liu, J.N. / Lei, K.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1chz.cif.gz | 26.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1chz.ent.gz | 16.5 KB | Display | PDB format |
PDBx/mmJSON format | 1chz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/1chz ftp://data.pdbj.org/pub/pdb/validation_reports/ch/1chz | HTTPS FTP |
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-Related structure data
Related structure data | 1snbS 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: 7222.237 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mesobuthus martensii (Chinese scorpion) / Organ: TAIL / Tissue: GLAND / References: UniProt: P58488 |
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#2: Chemical | ChemComp-CL / |
#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: 1.83 Å3/Da / Density % sol: 31.51 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 / Details: pH 7.5 | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
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 / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→20 Å / Num. obs: 5004 / % possible obs: 90 % / Redundancy: 2.4 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.1 |
Reflection shell | Resolution: 1.76→1.82 Å / % possible all: 55.3 |
Reflection | *PLUS % possible obs: 90 % / Num. measured all: 11634 / Rmerge(I) obs: 0.1 |
Reflection shell | *PLUS % possible obs: 55.3 % / Rmerge(I) obs: 0.34 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SNB Resolution: 1.76→20 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: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.22 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.76→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.76→1.82 Å / Total num. of bins used: 10 /
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 23 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.364 / % reflection Rfree: 10 % / Rfactor Rwork: 0.3 |