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Open data
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Basic information
Entry | Database: PDB / ID: 8alp | ||||||
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Title | Botulinum neurotoxin A6 cell binding domain crystal form II | ||||||
![]() | Bont/A1 | ||||||
![]() | TOXIN / Botulinum neurotoxin / cell binding domain / hinge motion | ||||||
Function / homology | ![]() protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gregory, K.S. / Acharya, K.R. / Liu, S.M. | ||||||
Funding support | 1items
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![]() | ![]() Title: Crystal Structures of the Clostridium botulinum Neurotoxin A6 Cell Binding Domain Alone and in Complex with GD1a Reveal Significant Conformational Flexibility. Authors: Gregory, K.S. / Newell, A.R. / Mojanaga, O.O. / Liu, S.M. / Acharya, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.3 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 467.1 KB | Display | |
Data in XML | ![]() | 17.2 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8agkC ![]() 6twoS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 50681.645 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.63 % |
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Crystal grow | Temperature: 289.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M magnesium acetate tetrahydrate, 0.1 M MES pH 6.5, 12% w/v of 50% PEG smear medium (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, ...Details: 0.1 M magnesium acetate tetrahydrate, 0.1 M MES pH 6.5, 12% w/v of 50% PEG smear medium (4.55% v/v PEG 400, 4.55% v/v PEG 500 MME, 4.55% v/v PEG 600, 4.55% w/v PEG 1000, 4.55% w/v PEG 2000, 4.55% w/v PEG 3350, 4.55% w/v PEG 4000, 4.55% w/v PEG 5000 MME, 4.55% w/v PEG 6000, 4.55% w/v PEG 8000, 4.55% w/v PEG 10000) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Oct 16, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→118.55 Å / Num. obs: 60147 / % possible obs: 99.6 % / Redundancy: 26.3 % / CC1/2: 1 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.023 / Net I/σ(I): 12 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 5.68 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2894 / CC1/2: 0.33 / Rpim(I) all: 1.125 / % possible all: 97.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6TWO Resolution: 1.5→65.705 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / WRfactor Rfree: 0.286 / WRfactor Rwork: 0.246 / SU B: 2.573 / SU ML: 0.091 / Average fsc free: 0.8076 / Average fsc work: 0.8164 / Cross valid method: FREE R-VALUE / ESU R: 0.104 / ESU R Free: 0.106 Details: Hydrogens have been added in their riding positions
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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 BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.142 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→65.705 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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