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Yorodumi- PDB-7lou: Crystal structure of Clostridium difficile Toxin B (TcdB) glucosy... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lou | ||||||
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Title | Crystal structure of Clostridium difficile Toxin B (TcdB) glucosyltransferase in complex with UDP and isofagomine | ||||||
Components | Glucosyltransferase TcdB | ||||||
Keywords | TRANSFERASE/Inhibitor / inhibitors / TcdB / toxin / Kinetic isotope effects / KIEs / drug design / TRANSFERASE / TRANSFERASE-Inhibitor complex | ||||||
Function / homology | Function and homology information glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Harijan, R.K. / Paparella, A.S. / Aboulache, B.L. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: Nat Commun / Year: 2021 Title: Inhibition of Clostridium difficile TcdA and TcdB toxins with transition state analogues. Authors: Paparella, A.S. / Aboulache, B.L. / Harijan, R.K. / Potts, K.S. / Tyler, P.C. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lou.cif.gz | 247.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lou.ent.gz | 195.4 KB | Display | PDB format |
PDBx/mmJSON format | 7lou.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/7lou ftp://data.pdbj.org/pub/pdb/validation_reports/lo/7lou | HTTPS FTP |
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-Related structure data
Related structure data | 7lovC 5uqmS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 0 / Auth seq-ID: 2 - 540 / Label seq-ID: 3 - 541
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 64313.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB / Production host: Escherichia coli (E. coli) References: UniProt: P18177, Transferases; Glycosyltransferases; Hexosyltransferases |
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-Non-polymers , 5 types, 512 molecules
#2: Chemical | ChemComp-EDO / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.54 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 200 mM Ammonium phosphate monobasic, 20% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Apr 10, 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: 1.82→121.34 Å / Num. obs: 115828 / % possible obs: 99.8 % / Redundancy: 7.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 1.82→1.85 Å / Redundancy: 6 % / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1 / Num. unique obs: 5500 / CC1/2: 0.62 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5UQM Resolution: 1.82→104.61 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.595 / SU ML: 0.152 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 133.05 Å2 / Biso mean: 43.184 Å2 / Biso min: 26.17 Å2
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Refinement step | Cycle: final / Resolution: 1.82→104.61 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 18074 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.82→1.867 Å / Rfactor Rfree error: 0
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