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Open data
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Basic information
Entry | Database: PDB / ID: 6apy | ||||||
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Title | Scabin (W128Y) toxin from Streptomyces scabies | ||||||
![]() | Scabin | ||||||
![]() | TOXIN / transferase / bacterial toxin | ||||||
Function / homology | : / nucleotide binding / Putative secreted protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lyons, B. / Lidster, T. / Merrill, A.R. | ||||||
![]() | ![]() Title: Characterization of the catalytic signature of Scabin toxin, a DNA-targeting ADP-ribosyltransferase. Authors: Lyons, B. / Lugo, M.R. / Carlin, S. / Lidster, T. / Merrill, A.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 | ![]() | 112.4 KB | Display | ![]() |
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PDB format | ![]() | 85.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 425.6 KB | Display | ![]() |
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Full document | ![]() | 425.6 KB | Display | |
Data in XML | ![]() | 9.3 KB | Display | |
Data in CIF | ![]() | 12.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5tlbC ![]() 5uvqC ![]() 5dazS 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 on special symmetry positions |
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Components
#1: Protein | Mass: 21834.135 Da / Num. of mol.: 1 / Mutation: W128Y Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 87.22 / Gene: SCAB_27771 / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG400, 0.1 M MES, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Dec 12, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→37.34 Å / Num. obs: 31670 / % possible obs: 99.8 % / Redundancy: 4.2 % / Biso Wilson estimate: 18.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.024 / Rsym value: 0.049 / Net I/σ(I): 17.81 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 5DAZ Resolution: 1.5→37.34 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso mean: 24.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→37.34 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection Rfree: 5 %
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