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Yorodumi- PDB-7d6r: Crystal structure of the Stx2a complexed with MMA betaAla peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 7d6r | ||||||
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Title | Crystal structure of the Stx2a complexed with MMA betaAla peptide | ||||||
Components |
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Keywords | TOXIN / Shiga toxin | ||||||
Function / homology | Function and homology information hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / metabolic process / toxin activity / negative regulation of translation / extracellular region Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Takahashi, M. / Tamada, M. / Hibino, M. / Senda, M. / Okuda, A. / Miyazawa, A. / Senda, T. / Nishikawa, K. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Commun Biol / Year: 2021 Title: Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin. Authors: Watanabe-Takahashi, M. / Tamada, M. / Senda, M. / Hibino, M. / Shimizu, E. / Okuta, A. / Miyazawa, A. / Senda, T. / Nishikawa, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7d6r.cif.gz | 178.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7d6r.ent.gz | 113.6 KB | Display | PDB format |
PDBx/mmJSON format | 7d6r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d6/7d6r ftp://data.pdbj.org/pub/pdb/validation_reports/d6/7d6r | HTTPS FTP |
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-Related structure data
Related structure data | 7d6qC 1r4pS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 33228.215 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stx2a / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XBV2, rRNA N-glycosylase | ||||||||||
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#2: Protein | Mass: 7824.590 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stxII, stx2B, stx2B_2, stx2dB, stx2vB, stxB2, vtx2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DJJ2 #3: Protein/peptide | | Mass: 1251.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) #4: Chemical | ChemComp-1PS / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | Sequence details | Chain G has amidation of C-terminus. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 4 M sodium formate, 100 mM MES pH 6.5, 50 mM 3-(1-Pyridinio)-1-propanesulfonate (PPS) |
-Data collection
Diffraction | Mean temperature: 95 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2015 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→73.25 Å / Num. obs: 97151 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 17.82 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.48 |
Reflection shell | Resolution: 1.6→1.69 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 6.37 / Num. unique obs: 14626 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1R4P Resolution: 1.6→73.24 Å / SU ML: 0.1484 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.624
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→73.24 Å
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Refine LS restraints |
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LS refinement shell |
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