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- PDB-1r4q: Shiga toxin -

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Basic information

Entry
Database: PDB / ID: 1r4q
TitleShiga toxin
Components
  • SHT cytotoxin A subunit
  • Shigella toxin chain B
KeywordsTOXIN / AB5 toxin
Function / homology
Function and homology information


hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / metabolic process / 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 / Enterotoxin / Ribosome-inactivating protein conserved site ...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 / Enterotoxin / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / 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 / Molecular replacement, SIR, averaging / Resolution: 2.5 Å
AuthorsFraser, M.E. / Fujinaga, M. / Cherney, M.M. / Melton-Celsa, A.R. / Twiddy, E.M. / O'Brien, A.D. / James, M.N.G.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structure of Shiga Toxin Type 2 (Stx2) from Escherichia coli O157:H7.
Authors: Fraser, M.E. / Fujinaga, M. / Cherney, M.M. / Melton-Celsa, A.R. / Twiddy, E.M. / O'Brien, A.D. / James, M.N.G.
History
DepositionOct 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Remark 999sequence the authors maintain that the sequence database reference is incorrect at this position

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SHT cytotoxin A subunit
L: SHT cytotoxin A subunit
B: Shigella toxin chain B
C: Shigella toxin chain B
D: Shigella toxin chain B
E: Shigella toxin chain B
F: Shigella toxin chain B
G: Shigella toxin chain B
H: Shigella toxin chain B
I: Shigella toxin chain B
J: Shigella toxin chain B
K: Shigella toxin chain B


Theoretical massNumber of molelcules
Total (without water)141,51512
Polymers141,51512
Non-polymers00
Water82946
1
A: SHT cytotoxin A subunit
B: Shigella toxin chain B
C: Shigella toxin chain B
D: Shigella toxin chain B
E: Shigella toxin chain B
F: Shigella toxin chain B


Theoretical massNumber of molelcules
Total (without water)70,7586
Polymers70,7586
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9240 Å2
ΔGint-41 kcal/mol
Surface area23550 Å2
MethodPISA
2
L: SHT cytotoxin A subunit
G: Shigella toxin chain B
H: Shigella toxin chain B
I: Shigella toxin chain B
J: Shigella toxin chain B
K: Shigella toxin chain B


Theoretical massNumber of molelcules
Total (without water)70,7586
Polymers70,7586
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9370 Å2
ΔGint-45 kcal/mol
Surface area23680 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22620 Å2
ΔGint-80 kcal/mol
Surface area43220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.000, 147.180, 82.850
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 SHT cytotoxin A subunit / rRNA N-glycosidase


Mass: 32264.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Plasmid: PSHT23 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101
References: UniProt: Q7BQ99, UniProt: Q9FBI2*PLUS, rRNA N-glycosylase
#2: Protein
Shigella toxin chain B


Mass: 7698.634 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Plasmid: PSHT23 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: Q7BQ98
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: SODIUM CITRATE, ETHANOL, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
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→98.6 Å / Num. all: 56837 / Num. obs: 53525 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.66 Å / % possible all: 75.6

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Processing

Software
NameClassification
WEISdata scaling
BIOMOLdata reduction
BIOMOLmodel building
CNSrefinement
WEISdata reduction
BIOMOLdata scaling
RefinementMethod to determine structure: Molecular replacement, SIR, averaging
Resolution: 2.5→98.6 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2566 2747 random
Rwork0.1994 --
all0.202 56837 -
obs0.202 53525 -
Refinement stepCycle: LAST / Resolution: 2.5→98.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9679 0 0 46 9725
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_angle_deg1.9
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.383 361 -
Rwork0.375 --
obs-7061 75.6 %

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