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- PDB-1r4p: Shiga toxin type 2 -

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Basic information

Entry
Database: PDB / ID: 1r4p
TitleShiga toxin type 2
Components(shiga-like toxin type II ...) x 2
KeywordsTOXIN / AB5 toxin
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / hemolysis by symbiont of host erythrocytes / 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 / 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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / FORMIC ACID / Shiga-like toxin 2 subunit A / Shiga-like toxin 2 subunit B / Shiga-like toxin II B subunit / Shiga-like toxin 2 subunit A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.77 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: shiga-like toxin type II A subunit
B: shiga-like toxin type II B subunit
C: shiga-like toxin type II B subunit
D: shiga-like toxin type II B subunit
E: shiga-like toxin type II B subunit
F: shiga-like toxin type II B subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,27235
Polymers72,3516
Non-polymers1,92129
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16970 Å2
ΔGint-52 kcal/mol
Surface area21650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.960, 143.960, 59.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Shiga-like toxin type II ... , 2 types, 6 molecules ABCDEF

#1: Protein shiga-like toxin type II A subunit / SLTII A subunit


Mass: 33228.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: STX2A / Plasmid: pLPSH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha
References: UniProt: Q9R398, UniProt: P09385*PLUS, rRNA N-glycosylase
#2: Protein
shiga-like toxin type II B subunit / SLTII B subunit


Mass: 7824.590 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: STX2B / Plasmid: pLPSH3 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: Q57249, UniProt: P09386*PLUS

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Non-polymers , 5 types, 540 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM, PPS


Mass: 201.243 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H11NO3S
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4 M sodium formate, 0.1 M MES, 50 mM 3-(1-pyridino)-1-propanesulfonate, 1% ethylene glycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 20, 2000 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→25.1 Å / Num. all: 68504 / Num. obs: 66890 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.77→1.88 Å / % possible all: 95

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
ALMNBRUTEmodel building
CNSrefinement
CCP4(ALMNphasing
BRUTEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→25.1 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.1837 3376 random
Rwork0.1512 --
all0.153 68504 -
obs0.153 66890 -
Refinement stepCycle: LAST / Resolution: 1.77→25.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 77 559 5617
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_angle_deg2
LS refinement shellResolution: 1.77→1.88 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.239 557 -
Rwork0.204 --
obs-10771 95 %

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