+Open data
-Basic information
Entry | Database: PDB / ID: 3nds | ||||||
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Title | Crystal structure of engineered Naja Nigricollis toxin alpha | ||||||
Components | Short neurotoxin 1 | ||||||
Keywords | TOXIN / Disulfide pairing / folding intermediates / Three finger toxin fold / Snake toxin / venom | ||||||
Function / homology | Function and homology information acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å | ||||||
Authors | Stura, E.A. / Drevet, P. / Gregory, G. / Gallopin, M. / Vandame, M. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2010 Title: Conformational exchange is critical for the productivity of an oxidative folding intermediate with buried free cysteines. Authors: Gross, G. / Gallopin, M. / Vandame, M. / Couprie, J. / Stura, E. / Zinn-Justin, S. / Drevet, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nds.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nds.ent.gz | 39.2 KB | Display | PDB format |
PDBx/mmJSON format | 3nds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nds_validation.pdf.gz | 457 KB | Display | wwPDB validaton report |
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Full document | 3nds_full_validation.pdf.gz | 463.4 KB | Display | |
Data in XML | 3nds_validation.xml.gz | 8 KB | Display | |
Data in CIF | 3nds_validation.cif.gz | 10.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nd/3nds ftp://data.pdbj.org/pub/pdb/validation_reports/nd/3nds | HTTPS FTP |
-Related structure data
Related structure data | 1iq9S 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: 6892.859 Da / Num. of mol.: 1 / Fragment: ENGINEERED TOXIN ALPHA / Mutation: inserted Ser 18 / Source method: obtained synthetically Details: This sequence has ser18 inserted in the alpha toxin from Naja nigricollis. References: UniProt: P01426 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: 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: 2.17 Å3/Da / Density % sol: 43.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25 mg/ml toxin alpha-62 mutant lyophilized (2mg resuspende in 80 l 50mM sodium acetate, pH 4.25, 0.02% NaN3. precipitant: 1.8M A.S., 5% MPD, 80mM Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9794913 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2006 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SAGITALLY FOCUSED Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9794913 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.2→40.83 Å / Num. all: 19632 / Num. obs: 19396 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 13.3 % / Biso Wilson estimate: 10.4 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.07 / Net I/σ(I): 28.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1IQ9 Resolution: 1.2→28.755 Å / SU ML: 0.06 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 1.36 / σ(I): 0 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.895 Å2 / ksol: 0.426 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.2→28.755 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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