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- PDB-1dtp: THE STRUCTURE OF THE ISOLATED CATALYTIC DOMAIN OF DIPHTHERIA TOXIN -

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Basic information

Entry
Database: PDB / ID: 1dtp
TitleTHE STRUCTURE OF THE ISOLATED CATALYTIC DOMAIN OF DIPHTHERIA TOXIN
ComponentsDIPHTHERIA TOXIN
KeywordsTOXIN
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
Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 ...Diphtheria toxin, receptor-binding domain / Diphtheria toxin, receptor-binding domain superfamily / Diphtheria toxin, R domain / Diphtheria toxin (NAD+-dipthamide ADP-ribosyltransferase) / Diphtheria toxin, catalytic domain / Diphtheria toxin, C domain / Diphtheria toxin, translocation domain superfamily / Diphtheria toxin, T domain / Diphtheria Toxin; domain 1 / Diphtheria Toxin, domain 1 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE / Diphtheria toxin
Similarity search - Component
Biological speciesCorynephage beta (virus)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsWeiss, 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
DepositionSep 8, 1994Processing site: BNL
Revision 1.0Nov 1, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4282
Polymers20,7751
Non-polymers6531
Water1448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.700, 43.900, 73.900
Angle α, β, γ (deg.)90.00, 101.50, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DIPHTHERIA TOXIN


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 / ADENYLYL-3'-5'-PHOSPHO-URIDINE-3'-MONOPHOSPHATE


Mass: 653.387 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H25N7O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity 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
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
19 mg/mlprotein1drop
225-75 mM1reservoirMgCl2
30-5 mM1reservoirCaCl2
45 mMdithiothreitol1reservoir
528 %PEG33501reservoirprecipitant
6100 mM1reservoirNaOAc

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative 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

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.197 -
obs0.197 5228
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 43 8 1505
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.023
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg4.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
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
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg1.7

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