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Open data
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Basic information
Entry | Database: PDB / ID: 4x9z | ||||||
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Title | Dimeric conotoxin alphaD-GeXXA | ||||||
![]() | alphaD-conotoxin GeXXA from the venom of Conus generalis | ||||||
![]() | TOXIN / alpha-conotoxin / GeXXA / Nicotinic acetylcholine receptor / homodimer | ||||||
Function / homology | host cell postsynaptic membrane / toxin activity / extracellular region / Alpha-conotoxin GeXXA![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Xu, S. / Zhang, T. / Kompella, S. / Adams, D. / Ding, J. / Wang, C. | ||||||
![]() | ![]() Title: Conotoxin alpha D-GeXXA utilizes a novel strategy to antagonize nicotinic acetylcholine receptors Authors: Xu, S. / Zhang, T. / Kompella, S.N. / Yan, M. / Lu, A. / Wang, Y. / Shao, X. / Chi, C. / Adams, D.J. / Ding, J. / Wang, C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 50.1 KB | Display | ![]() |
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PDB format | ![]() | 39 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | biological unit is the same as asym. |
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Components
#1: Protein/peptide | Mass: 5644.727 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: venom / Source: (natural) ![]() #2: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEB | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1M citrate acid, 10% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 13989 / % possible obs: 92.8 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 47.5 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.418 / Mean I/σ(I) obs: 4.6 / % possible all: 94.4 |
-Phasing
Phasing | Method: AB_INITIO |
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Processing
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 1.5→41.51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.454 / SU ML: 0.056 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.1 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 128.71 Å2 / Biso mean: 40.899 Å2 / Biso min: 16.18 Å2
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Refinement step | Cycle: final / Resolution: 1.5→41.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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