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Yorodumi- PDB-1ddt: THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ddt | ||||||
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Title | THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION | ||||||
Components | DIPHTHERIA TOXIN | ||||||
Keywords | TOXIN | ||||||
Function / homology | Function and homology information NAD+-diphthamide ADP-ribosyltransferase / NAD+-diphthamide ADP-ribosyltransferase activity / Uptake and function of diphtheria toxin / protein transmembrane transporter activity / nucleotidyltransferase activity / toxin activity / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Corynephage beta (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Bennett, M.J. / Eisenberg, D. | ||||||
Citation | Journal: Protein Sci. / Year: 1994 Title: Refined structure of dimeric diphtheria toxin at 2.0 A resolution. Authors: Bennett, M.J. / Choe, S. / Eisenberg, D. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Domain Swapping: Entangling Alliances between Proteins Authors: Bennett, M.J. / Choe, S. / Eisenberg, D. #2: Journal: Nature / Year: 1992 Title: The Crystal Structure of Diphtheria Toxin Authors: Choe, S. / Bennett, M.J. / Fujii, G. / Curmi, P.M.G. / Kantardjieff, K.A. / Collier, R.J. / Eisenberg, D. | ||||||
History |
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Remark 700 | SHEET SHEET R1 IS NOT A CLOSED BARREL, BUT IS CLOSED ON ONE SIDE AND FLATTENED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ddt.cif.gz | 117.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ddt.ent.gz | 95.6 KB | Display | PDB format |
PDBx/mmJSON format | 1ddt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ddt_validation.pdf.gz | 791 KB | Display | wwPDB validaton report |
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Full document | 1ddt_full_validation.pdf.gz | 807.8 KB | Display | |
Data in XML | 1ddt_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | 1ddt_validation.cif.gz | 39.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dd/1ddt ftp://data.pdbj.org/pub/pdb/validation_reports/dd/1ddt | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 58411.359 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynephage beta (virus) / Genus: Lambda-like viruses / References: UniProt: P00588 |
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#2: Chemical | ChemComp-APU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55.02 % | ||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software |
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Refinement | Resolution: 2→10 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.195 / Rfactor Rwork: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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