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- PDB-1ddt: THE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROM... -

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Basic information

Entry
Database: PDB / ID: 1ddt
TitleTHE REFINED STRUCTURE OF DIMERIC DIPHTHERIA TOXIN AT 2.0 ANGSTROMS RESOLUTION
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, translocation domain / Diphtheria toxin, receptor-binding domain / 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, translocation domain / Diphtheria toxin, receptor-binding domain / 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 / Globin-like / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / 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 Å
AuthorsBennett, 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
DepositionMar 1, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 2.0Nov 20, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET SHEET R1 IS NOT A CLOSED BARREL, BUT IS CLOSED ON ONE SIDE AND FLATTENED.

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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)59,0652
Polymers58,4111
Non-polymers6531
Water7,296405
1
A: DIPHTHERIA TOXIN
hetero molecules

A: DIPHTHERIA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1294
Polymers116,8232
Non-polymers1,3072
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area10560 Å2
ΔGint-30 kcal/mol
Surface area40440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.640, 92.560, 65.580
Angle α, β, γ (deg.)90.00, 94.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-669-

HOH

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Components

#1: Protein DIPHTHERIA TOXIN


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
#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.: 405 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %(w/v)PEG80001reservoir
20.43 M1reservoirNaCl
30.043 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.195 -
obs0.195 37727
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 43 405 4469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.6
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
Rfactor obs: 0.195 / Rfactor Rwork: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d2.6
X-RAY DIFFRACTIONx_dihedral_angle_d25.8
X-RAY DIFFRACTIONx_dihedral_angle_deg2

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