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- PDB-1mdt: THE REFINED STRUCTURE OF MONOMERIC DIPHTHERIA TOXIN AT 2.3 ANGSTR... -

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Basic information

Entry
Database: PDB / ID: 1mdt
TitleTHE REFINED STRUCTURE OF MONOMERIC DIPHTHERIA TOXIN AT 2.3 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: 2.3 Å
AuthorsBennett, M.J. / Eisenberg, D.
Citation
Journal: Protein Sci. / Year: 1994
Title: Refined structure of monomeric diphtheria toxin at 2.3 A resolution.
Authors: Bennett, M.J. / 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.
History
DepositionMar 21, 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: Version format compliance
Revision 1.3Jun 5, 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
Remark 700SHEET SHEET R1 IS NOT A CLOSED BARREL, BUT IT IS CLOSED ON ONE SIDE AND FLATTENED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIPHTHERIA TOXIN
B: DIPHTHERIA TOXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,1294
Polymers116,8232
Non-polymers1,3072
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)168.500, 135.500, 47.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9995, -0.0296, -0.0078), (-0.0297, 0.9996, 0.0027), (0.0078, 0.0029, -1)
Vector: -67.1061, -1.5167, 93.8764)

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Components

#1: Protein DIPHTHERIA TOXIN


Mass: 58411.359 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C19H25N7O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.3 Å3/Da / Density % sol: 46.42 %
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: microseeding and macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
217 %(w/v)PEG80001reservoir
31.0 M1reservoirNaCl
40.05 MTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementResolution: 2.3→10 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.207 --
obs-42844 88.8 %
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8042 0 86 396 8524
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.022
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.4
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d2.4
X-RAY DIFFRACTIONo_dihedral_angle_d25.8
X-RAY DIFFRACTIONo_dihedral_angle_deg2

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