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- PDB-7k7d: Crystal structure of diphtheria toxin from crystals obtained at pH 6.0 -
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Open data
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Basic information
Entry | Database: PDB / ID: 7k7d | |||||||||
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Title | Crystal structure of diphtheria toxin from crystals obtained at pH 6.0 | |||||||||
![]() | Diphtheria toxin | |||||||||
![]() | TOXIN / diptheria toxin / pH dependent conformational changes | |||||||||
Function / homology | ![]() NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / toxin activity / extracellular space / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() ![]() | |||||||||
![]() | Lovell, S. / Kashipathy, M.M. / Battaile, K.P. / Rodnin, M.V. / Ladokhin, A.S. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of the Diphtheria Toxin at Acidic pH: Implications for the Conformational Switching of the Translocation Domain. Authors: Rodnin, M.V. / Kashipathy, M.M. / Kyrychenko, A. / Battaile, K.P. / Lovell, S. / Ladokhin, A.S. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.9 KB | Display | ![]() |
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PDB format | ![]() | 160.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.8 KB | Display | ![]() |
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Full document | ![]() | 453.2 KB | Display | |
Data in XML | ![]() | 36.3 KB | Display | |
Data in CIF | ![]() | 51.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k7bC ![]() 7k7cC ![]() 7k7eC ![]() 1ddtS S: Starting model for refinement C: citing same article ( |
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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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Components
#1: Protein | Mass: 58744.828 Da / Num. of mol.: 2 / Fragment: Full Length / Mutation: K51E, E148K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52.75 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 10% (w/v) PEG 10000, 0.1 M magnesium acetate, 0.1 M MES |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→46.57 Å / Num. obs: 67346 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Net I/σ(I): 10.7 / Num. measured all: 236012 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1DDT Resolution: 2.1→36.427 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 31.23 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.77 Å2 / Biso mean: 56.0176 Å2 / Biso min: 27.59 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→36.427 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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