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- PDB-2ga4: Stx2 with adenine -

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Basic information

Entry
Database: PDB / ID: 2ga4
TitleStx2 with adenine
Components(Shiga-like toxin II subunit ...) x 2
KeywordsTOXIN / AB5-toxin
Function / homology
Function and homology information


symbiont-mediated modulation of host virulence / 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
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / ADENINE / FORMIC ACID / Shiga-like toxin 2 subunit A / Shiga-like toxin 2 subunit B
Similarity search - Component
Biological speciesEnterobacteria phage 933W (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsFraser, M.E.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Binding of adenine to Stx2, the protein toxin from Escherichia coli O157:H7.
Authors: Fraser, M.E. / Cherney, M.M. / Marcato, P. / Mulvey, G.L. / Armstrong, G.D. / James, M.N.
History
DepositionMar 7, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)73,69822
Polymers72,3516
Non-polymers1,34716
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14970 Å2
ΔGint-59 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.550, 144.550, 59.420
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 II subunit ... , 2 types, 6 molecules ABCDEF

#1: Protein Shiga-like toxin II subunit A / Verotoxin 2 subunit A / rRNA N-glycosidase / SLT-IIA


Mass: 33228.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage 933W (virus) / Species: Enterobacteria phage 933W sensu lato / Strain: C600 933W / References: UniProt: P09385, rRNA N-glycosylase
#2: Protein
Shiga-like toxin II subunit B / Verotoxin 2 subunit B / SLT- IIB


Mass: 7824.590 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage 933W (virus) / Species: Enterobacteria phage 933W sensu lato / Strain: C600 933W / References: UniProt: P09386

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Non-polymers , 6 types, 558 molecules

#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H5N5
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / 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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4 M sodium formate, 0.1 M 2-morpholinoethanesulfonic acid, 50 mM 3-(1-pyridino)-1-propanesulfonate, 3% ethylene glycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 10, 2004
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.8→200 Å / Num. all: 68743 / Num. obs: 68743 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.077 / Χ2: 0.944 / Net I/σ(I): 9.4
Reflection shellResolution: 1.8→1.83 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 3402 / Χ2: 0.331 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
XFITdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→200 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3275 5 %Random, but same as 1R4P
Rwork0.156 ---
all0.157 65741 --
obs0.157 65741 99.9 %-
Solvent computationBsol: 40.497 Å2
Displacement parametersBiso mean: 19.56 Å2
Baniso -1Baniso -2Baniso -3
1-2.281 Å20.382 Å20 Å2
2--2.281 Å20 Å2
3----4.562 Å2
Refinement stepCycle: LAST / Resolution: 1.8→200 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4977 0 71 557 5605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_bond_d0.016
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4PPS_par.txt
X-RAY DIFFRACTION5ade_xplor_par.txt

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