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Open data
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Basic information
Entry | Database: PDB / ID: 6u3u | ||||||
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Title | Crystal Structure of Shiga Toxin 2K | ||||||
![]() | (Shiga toxin 2K subunit ...) x 2 | ||||||
![]() | TOXIN / Shiga Toxin / AB5 Toxin / Toxoid | ||||||
Function / homology | ![]() symbiont-mediated hemolysis of host erythrocyte / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, Y.Z. / He, X.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural and Functional Characterization of Stx2k, a New Subtype of Shiga Toxin 2. Authors: Hughes, A.C. / Zhang, Y. / Bai, X. / Xiong, Y. / Wang, Y. / Yang, X. / Xu, Q. / He, X. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 464 KB | Display | ![]() |
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PDB format | ![]() | 386.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 501.4 KB | Display | ![]() |
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Full document | ![]() | 508.8 KB | Display | |
Data in XML | ![]() | 43.3 KB | Display | |
Data in CIF | ![]() | 60.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1r4pS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Shiga toxin 2K subunit ... , 2 types, 12 molecules BACDEHIFGJKL
#1: Protein | Mass: 33038.961 Da / Num. of mol.: 2 / Mutation: E167Q Source method: isolated from a genetically manipulated source Details: E167Q / Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 7748.584 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: vtx2B, stx2B, stx2B_2, BvCmsKKP036_03423, BvCmsNSP045_04912 Production host: ![]() ![]() References: UniProt: Q4PS70 |
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-Non-polymers , 4 types, 126 molecules 






#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-ZN / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1M HEPES, pH 7.5, 10% w/v PEG 8000, 15% Ethylene glycol |
-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: Feb 13, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.039→107.059 Å / Num. obs: 94159 / % possible obs: 93.6 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 13 / Num. measured all: 328715 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1R4P Resolution: 2.287→52.076 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.91
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 191.64 Å2 / Biso mean: 75.3925 Å2 / Biso min: 39.69 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.287→52.076 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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