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- PDB-1dm0: SHIGA TOXIN -

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Basic information

Entry
Database: PDB / ID: 1dm0
TitleSHIGA TOXIN
Components
  • SHIGA TOXIN A SUBUNIT
  • SHIGA TOXIN B SUBUNIT
KeywordsTOXIN / AB5 STRUCTURE / POLYPEPTIDE A / BLOCKING / ACTIVE SITE
Function / homology
Function and homology information


symbiont-mediated hemolysis of host erythrocyte / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #70 / Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Enterotoxin / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Few Secondary Structures / Irregular / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Shiga toxin subunit B / rRNA N-glycosylase / Shiga toxin subunit A
Similarity search - Component
Biological speciesShigella dysenteriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsFraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N.
Citation
Journal: Nat.Struct.Biol. / Year: 1994
Title: Crystal structure of the holotoxin from Shigella dysenteriae at 2.5 A resolution.
Authors: Fraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N.
#1: Journal: Protein Toxin Structure, Parker, M.W., Ed. / Year: 1996
Title: X-ray Crystal Structure of the Shiga Toxin
Authors: Fraser, M.E. / Chernaia, M.M. / Kozlov, Y.V. / James, M.N.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Purification and Crystallization of Shiga Toxin from Shigella dysenteriae
Authors: Kozlov, Y.V. / Chernaia, M.M. / Fraser, M.E. / James, M.N.
History
DepositionDec 13, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHIGA TOXIN A SUBUNIT
L: SHIGA TOXIN A SUBUNIT
B: SHIGA TOXIN B SUBUNIT
C: SHIGA TOXIN B SUBUNIT
D: SHIGA TOXIN B SUBUNIT
E: SHIGA TOXIN B SUBUNIT
F: SHIGA TOXIN B SUBUNIT
G: SHIGA TOXIN B SUBUNIT
H: SHIGA TOXIN B SUBUNIT
I: SHIGA TOXIN B SUBUNIT
J: SHIGA TOXIN B SUBUNIT
K: SHIGA TOXIN B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)140,11012
Polymers140,11012
Non-polymers00
Water1,11762
1
A: SHIGA TOXIN A SUBUNIT
B: SHIGA TOXIN B SUBUNIT
C: SHIGA TOXIN B SUBUNIT
D: SHIGA TOXIN B SUBUNIT
E: SHIGA TOXIN B SUBUNIT
F: SHIGA TOXIN B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)70,0556
Polymers70,0556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-45 kcal/mol
Surface area23120 Å2
MethodPISA
2
L: SHIGA TOXIN A SUBUNIT
G: SHIGA TOXIN B SUBUNIT
H: SHIGA TOXIN B SUBUNIT
I: SHIGA TOXIN B SUBUNIT
J: SHIGA TOXIN B SUBUNIT
K: SHIGA TOXIN B SUBUNIT


Theoretical massNumber of molelcules
Total (without water)70,0556
Polymers70,0556
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-42 kcal/mol
Surface area23140 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21090 Å2
ΔGint-81 kcal/mol
Surface area42230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.050, 147.460, 83.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SHIGA TOXIN A SUBUNIT


Mass: 31561.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: Q7BQ99, UniProt: Q9FBI2*PLUS, rRNA N-glycosylase
#2: Protein
SHIGA TOXIN B SUBUNIT


Mass: 7698.634 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q7BQ98
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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 / Number of used crystals: 4

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.68 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: sodium citrate, ethanol, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Details: Kozlov, Y.Z., (1993) J. Mol. Biol., 232, 704.

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Oct 23, 1992
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→10 Å / Num. all: 47612 / Num. obs: 47612 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.67 Å / Num. unique all: 5446 / % possible all: 53.1
Reflection shell
*PLUS
% possible obs: 53.1 %

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Processing

Software
NameClassification
TNTrefinement
BIOMOLdata reduction
BRUTEmodel building
MLPHAREphasing
DEMONmodel building
X-PLORrefinement
WEISdata scaling
WEISdata reduction
BIOMOLdata scaling
BRUTEphasing
DEMONphasing
RefinementResolution: 2.5→10 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT dictionary / Details: Refinement with X-PLOR and TNT
RfactorNum. reflection% reflection
Rwork0.206 --
obs0.206 47612 83.1 %
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9476 0 0 62 9538
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.03
X-RAY DIFFRACTIONt_bond_d0.011
X-RAY DIFFRACTIONt_pseud_angle20.4
X-RAY DIFFRACTIONt_trig_c_planes0.007
X-RAY DIFFRACTIONt_gen_planes0.011
Software
*PLUS
Name: 'X-PLOR, TNT' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.4
X-RAY DIFFRACTIONx_plane_restr0.011

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