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- PDB-7d6r: Crystal structure of the Stx2a complexed with MMA betaAla peptide -

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Basic information

Entry
Database: PDB / ID: 7d6r
TitleCrystal structure of the Stx2a complexed with MMA betaAla peptide
Components
  • MMA betaAla peptide
  • Shiga toxin 2 B subunit
  • rRNA N-glycosylase
KeywordsTOXIN / Shiga toxin
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
Shiga-like toxin, subunit A / Shiga-like toxin, beta subunit / Shiga-like toxin beta subunit / 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
Similarity search - Domain/homology
3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / Shiga toxin 2 B subunit / rRNA N-glycosylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTakahashi, M. / Tamada, M. / Hibino, M. / Senda, M. / Okuda, A. / Miyazawa, A. / Senda, T. / Nishikawa, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP19am0101001 Japan
CitationJournal: Commun Biol / Year: 2021
Title: Identification of a peptide motif that potently inhibits two functionally distinct subunits of Shiga toxin.
Authors: Watanabe-Takahashi, M. / Tamada, M. / Senda, M. / Hibino, M. / Shimizu, E. / Okuta, A. / Miyazawa, A. / Senda, T. / Nishikawa, K.
History
DepositionOct 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2021Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: rRNA N-glycosylase
B: Shiga toxin 2 B subunit
C: Shiga toxin 2 B subunit
D: Shiga toxin 2 B subunit
E: Shiga toxin 2 B subunit
F: Shiga toxin 2 B subunit
G: MMA betaAla peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,40811
Polymers73,6037
Non-polymers8054
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14360 Å2
ΔGint-14 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.489, 146.489, 60.162
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein rRNA N-glycosylase / Shiga toxin 2 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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8XBV2, rRNA N-glycosylase
#2: Protein
Shiga toxin 2 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: stxII, stx2B, stx2B_2, stx2dB, stx2vB, stxB2, vtx2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q7DJJ2
#3: Protein/peptide MMA betaAla peptide


Mass: 1251.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-1PS / 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE / 1-(3-SULFOPROPYL) PYRIDINIUM / PPS


Mass: 201.243 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C8H11NO3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY
Sequence detailsChain G has amidation of C-terminus.

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4 M sodium formate, 100 mM MES pH 6.5, 50 mM 3-(1-Pyridinio)-1-propanesulfonate (PPS)

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 11, 2015
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.6→73.25 Å / Num. obs: 97151 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 17.82 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 21.48
Reflection shellResolution: 1.6→1.69 Å / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 6.37 / Num. unique obs: 14626

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R4P

1r4p


Resolution: 1.6→73.24 Å / SU ML: 0.1484 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.624
RfactorNum. reflection% reflection
Rfree0.1973 4858 5 %
Rwork0.1745 --
obs0.1756 97145 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→73.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4937 0 58 390 5385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00565131
X-RAY DIFFRACTIONf_angle_d0.76976963
X-RAY DIFFRACTIONf_chiral_restr0.0548782
X-RAY DIFFRACTIONf_plane_restr0.0046897
X-RAY DIFFRACTIONf_dihedral_angle_d5.2483647
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.24651610.20853063X-RAY DIFFRACTION100
1.62-1.640.22731600.19753039X-RAY DIFFRACTION100
1.64-1.660.21691610.19243055X-RAY DIFFRACTION100
1.66-1.680.22361620.19333073X-RAY DIFFRACTION100
1.68-1.70.2271610.19063056X-RAY DIFFRACTION100
1.7-1.720.21271620.18543094X-RAY DIFFRACTION100
1.72-1.750.22921600.18883029X-RAY DIFFRACTION99.97
1.75-1.770.23941620.1863073X-RAY DIFFRACTION99.97
1.77-1.80.20911610.18583062X-RAY DIFFRACTION99.97
1.8-1.830.17781600.18063048X-RAY DIFFRACTION99.94
1.83-1.860.20721610.17983056X-RAY DIFFRACTION100
1.86-1.90.23751610.1833050X-RAY DIFFRACTION100
1.9-1.930.19921630.19243104X-RAY DIFFRACTION99.79
1.93-1.970.21111590.17493028X-RAY DIFFRACTION100
1.97-2.020.19991630.17383082X-RAY DIFFRACTION100
2.02-2.060.24981620.1783086X-RAY DIFFRACTION100
2.06-2.110.21421610.17153049X-RAY DIFFRACTION99.94
2.11-2.170.18711620.17063081X-RAY DIFFRACTION100
2.17-2.240.21941610.17723072X-RAY DIFFRACTION99.94
2.24-2.310.191620.17323070X-RAY DIFFRACTION99.94
2.31-2.390.16831610.16853061X-RAY DIFFRACTION100
2.39-2.490.21321620.18033077X-RAY DIFFRACTION100
2.49-2.60.22331630.18563087X-RAY DIFFRACTION100
2.6-2.740.22311620.19213088X-RAY DIFFRACTION100
2.74-2.910.21551620.19283079X-RAY DIFFRACTION100
2.91-3.130.2051630.18343090X-RAY DIFFRACTION100
3.13-3.450.19881630.1733106X-RAY DIFFRACTION99.94
3.45-3.950.18321640.15613107X-RAY DIFFRACTION99.91
3.95-4.970.12911640.13713123X-RAY DIFFRACTION99.97
4.97-73.240.19551690.18313199X-RAY DIFFRACTION99.85

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