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Yorodumi- PDB-3dwp: Crystal structure of the B-subunit of the AB5 toxin from E. Coli ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dwp | |||||||||
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Title | Crystal structure of the B-subunit of the AB5 toxin from E. Coli with Neu5Gc | |||||||||
Components | Subtilase cytotoxin, subunit B | |||||||||
Keywords | TOXIN | |||||||||
Function / homology | OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Enterotoxin / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / identical protein binding / N-glycolyl-alpha-neuraminic acid / Subtilase SubB Function and homology information | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | |||||||||
Authors | Byres, E. / Paton, A.W. / Paton, J.C. / Lofling, J.C. / Smith, D.F. / Wilce, M.C.J. / Talbot, U.M. / Chong, D.C. / Yu, H. / Huang, S. ...Byres, E. / Paton, A.W. / Paton, J.C. / Lofling, J.C. / Smith, D.F. / Wilce, M.C.J. / Talbot, U.M. / Chong, D.C. / Yu, H. / Huang, S. / Chen, X. / Varki, N.M. / Varki, A. / Rossjohn, J. / Beddoe, T. | |||||||||
Citation | Journal: Nature / Year: 2008 Title: Incorporation of a non-human glycan mediates human susceptibility to a bacterial toxin Authors: Byres, E. / Paton, A.W. / Paton, J.C. / Lofling, J.C. / Smith, D.F. / Wilce, M.C.J. / Talbot, U.M. / Chong, D.C. / Yu, H. / Huang, S. / Chen, X. / Varki, N.M. / Varki, A. / Rossjohn, J. / Beddoe, T. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dwp.cif.gz | 132.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dwp.ent.gz | 108.8 KB | Display | PDB format |
PDBx/mmJSON format | 3dwp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3dwp_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 3dwp_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 3dwp_validation.xml.gz | 32.2 KB | Display | |
Data in CIF | 3dwp_validation.cif.gz | 43.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/3dwp ftp://data.pdbj.org/pub/pdb/validation_reports/dw/3dwp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLU / End label comp-ID: LYS / Refine code: 4 / Auth seq-ID: 1 - 115 / Label seq-ID: 1 - 115
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-Components
#1: Protein | Mass: 14033.598 Da / Num. of mol.: 5 / Fragment: residues in database 24-141 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: subB / Production host: Escherichia coli (E. coli) / References: UniProt: Q3ZTX8 #2: Sugar | ChemComp-NGC / #3: Chemical | ChemComp-1PE / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.2 Å3/Da / Density % sol: 61.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 16% PEG 3350, 100mM sodium cacodylate, 200mM ammonium fluoride, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→83.92 Å / Num. obs: 39693 |
Reflection shell | Resolution: 2.2→2.32 Å |
-Processing
Software | Name: REFMAC / Version: 5.2.0019 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→23.97 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.134 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.463 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→23.97 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 884 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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