+Open data
-Basic information
Entry | Database: PDB / ID: 7vhc | ||||||
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Title | Crystal structure of the STX2a complexed with AR4A 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) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Senda, M. / Takahashi, M. / Nishikawa, K. / Senda, T. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Sci Rep / Year: 2022 Title: A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin. Authors: Watanabe-Takahashi, M. / Senda, M. / Yoshino, R. / Hibino, M. / Hama, S. / Terada, T. / Shimizu, K. / 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 | 7vhc.cif.gz | 181.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vhc.ent.gz | 115.1 KB | Display | PDB format |
PDBx/mmJSON format | 7vhc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vh/7vhc ftp://data.pdbj.org/pub/pdb/validation_reports/vh/7vhc | HTTPS FTP |
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-Related structure data
Related structure data | 7vhdC 7vheC 7vhfC 7d6rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 786.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Chemical | ChemComp-1PS / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / Details: 4 M Sodium Formate, 100mM MES pH 6.5, 50 mM 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-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 4, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.86 Å / Num. obs: 68253 / % possible obs: 100 % / Redundancy: 21.2 % / Biso Wilson estimate: 16.2 Å2 / Rpim(I) all: 0.039 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.8→1.84 Å / Mean I/σ(I) obs: 3.1 / Num. unique obs: 4025 / Rpim(I) all: 0.039 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7D6R Resolution: 1.8→47.86 Å / SU ML: 0.1884 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.715 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 16.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→47.86 Å
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Refine LS restraints |
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LS refinement shell |
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