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Open data
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Basic information
Entry | Database: PDB / ID: 7s0z | ||||||
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Title | Structures of TcdB in complex with R-Ras | ||||||
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![]() | Hydrolase/Transferase / toxin / substrate / enzyme / Hydrolase-Transferase complex | ||||||
Function / homology | ![]() leukocyte differentiation / positive regulation of endothelial cell-matrix adhesion via fibronectin / Schwann cell migration / negative regulation of Schwann cell migration / positive regulation of vasculogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / face morphogenesis / Sema4D mediated inhibition of cell attachment and migration / host cell cytosol / glycosyltransferase activity ...leukocyte differentiation / positive regulation of endothelial cell-matrix adhesion via fibronectin / Schwann cell migration / negative regulation of Schwann cell migration / positive regulation of vasculogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / face morphogenesis / Sema4D mediated inhibition of cell attachment and migration / host cell cytosol / glycosyltransferase activity / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cysteine-type peptidase activity / positive regulation of endothelial cell migration / regulation of ERK1 and ERK2 cascade / host cell endosome membrane / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / positive regulation of angiogenesis / GDP binding / toxin activity / Ras protein signal transduction / focal adhesion / GTPase activity / lipid binding / protein-containing complex binding / GTP binding / host cell plasma membrane / proteolysis / extracellular exosome / extracellular region / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zheng, L. / Rongsheng, J. / Peng, C. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B. Authors: Liu, Z. / Zhang, S. / Chen, P. / Tian, S. / Zeng, J. / Perry, K. / Dong, M. / Jin, 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 | ![]() | 317 KB | Display | ![]() |
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PDB format | ![]() | 252.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 58.5 KB | Display | |
Data in CIF | ![]() | 80.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7s0yC ![]() 2fn4S ![]() 6oq7S 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 2 types, 4 molecules BACD
#1: Protein | Mass: 62642.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: M4NKV9, Transferases; Glycosyltransferases; Hexosyltransferases #2: Protein | Mass: 19945.336 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P10301, Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement |
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-Sugars , 1 types, 2 molecules ![](data/chem/img/GLC.gif)
#9: Sugar |
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-Non-polymers , 9 types, 588 molecules ![](data/chem/img/UDP.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NH4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/GDP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-NH4 / #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-PEG / | #8: Chemical | #10: Chemical | ChemComp-MG / #11: Chemical | #12: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M ammonium acetate, 0.1M sodium citrate tribasic dihydrate, pH 4.8, and 17% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→112.11 Å / Num. obs: 70923 / % possible obs: 98.9 % / Redundancy: 3.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.085 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 2.34→2.39 Å / Num. unique obs: 4599 / CC1/2: 0.693 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6OQ7,2FN4 Resolution: 2.34→76.02 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.922 / SU B: 8.499 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.403 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.61 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→76.02 Å
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