[English] 日本語
Yorodumi- PDB-1dtp: THE STRUCTURE OF THE ISOLATED CATALYTIC DOMAIN OF DIPHTHERIA TOXIN -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dtp | ||||||
---|---|---|---|---|---|---|---|
Title | THE STRUCTURE OF THE ISOLATED CATALYTIC DOMAIN OF DIPHTHERIA TOXIN | ||||||
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: 2.5 Å | ||||||
Authors | Weiss, M.S. / Eisenberg, D. | ||||||
Citation | Journal: Biochemistry / Year: 1995 Title: Structure of the isolated catalytic domain of diphtheria toxin. Authors: Weiss, M.S. / Blanke, S.R. / Collier, R.J. / Eisenberg, D. #1: Journal: To be Published Title: The Refined Structure of Dimeric Diphtheria Toxin at 2.0 Angstroms Resolution Authors: Bennett, M.J. / Choe, S. / Eisenberg, D. #2: Journal: To be Published Title: The Refined Structure of Monomeric Diphtheria Toxin Authors: Bennett, M.J. / Eisenberg, D. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994 Title: Domain Swapping: Entangling Alliances between Proteins Authors: Bennett, M.J. / Choe, S. / Eisenberg, D. #4: Journal: Nature / Year: 1992 Title: Three Domains for Three Functions: The Crystal Structure of Diphtheria Toxin Authors: Choe, S. / Bennett, M.J. / Fujii, G. / Curmi, P.M.G. / Kantardjeff, K.A. / Collier, R.J. / Eisenberg, D. #5: Journal: J.Biol.Chem. / Year: 1989 Title: X-Ray Grade Crystals of the Enzymatic Fragment of Diphtheria Toxin Authors: Kantardjeff, K. / Collier, R.J. / Eisenberg, D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dtp.cif.gz | 50.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dtp.ent.gz | 35.8 KB | Display | PDB format |
PDBx/mmJSON format | 1dtp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dtp_validation.pdf.gz | 766.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1dtp_full_validation.pdf.gz | 777.4 KB | Display | |
Data in XML | 1dtp_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | 1dtp_validation.cif.gz | 13.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dtp ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dtp | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20774.979 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 |
---|---|
#2: Chemical | ChemComp-APU / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.26 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / PH range low: 5.3 / PH range high: 4.7 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 5315 / % possible obs: 83.7 % / Rmerge(I) obs: 0.062 |
Reflection shell | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 2.8 Å / % possible obs: 80.4 % / Rmerge(I) obs: 0.189 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.5→10 Å / σ(F): 0 /
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection all: 5228 / Rfactor all: 0.197 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|