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- PDB-7vhf: Crystal structure of the STX2a complexed with RRA peptide -

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Basic information

Entry
Database: PDB / ID: 7vhf
TitleCrystal structure of the STX2a complexed with RRA peptide
Components
  • RRA 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSenda, M. / Takahashi, M. / Nishikawa, K. / Senda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
CitationJournal: Sci Rep / Year: 2022
Title: A unique peptide-based pharmacophore identifies an inhibitory compound against the A-subunit of Shiga toxin.
Authors: Watanabe-Takahashi, M. / Senda, M. / Yoshino, R. / Hibino, M. / Hama, S. / Terada, T. / Shimizu, K. / Senda, T. / Nishikawa, K.
History
DepositionSep 22, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Oct 16, 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: RRA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,65012
Polymers72,7537
Non-polymers8975
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14050 Å2
ΔGint-18 kcal/mol
Surface area22270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.171, 146.171, 60.514
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
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

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Protein , 2 types, 6 molecules ABCDEF

#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

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Protein/peptide , 1 types, 1 molecules G

#3: Protein/peptide RRA peptide


Mass: 401.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 434 molecules

#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: obtained synthetically / Formula: C8H11NO3S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 4 M Sodium Formate, 100mM MES pH 6.5, 50 mM PPS

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 4, 2018
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.75→47.85 Å / Num. obs: 74551 / % possible obs: 100 % / Redundancy: 20.9 % / Biso Wilson estimate: 15.42 Å2 / Net I/σ(I): 20.9
Reflection shellResolution: 1.75→1.78 Å

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D6R

7d6r


Resolution: 1.75→47.85 Å / SU ML: 0.166 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.826
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.186 3681 4.94 %
Rwork0.166 --
obs0.167 74504 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 1.75→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4950 0 58 429 5437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065102
X-RAY DIFFRACTIONf_angle_d0.8486907
X-RAY DIFFRACTIONf_dihedral_angle_d6.271711
X-RAY DIFFRACTIONf_chiral_restr0.056778
X-RAY DIFFRACTIONf_plane_restr0.008886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.23721450.20152700X-RAY DIFFRACTION100
1.77-1.80.24411280.19512754X-RAY DIFFRACTION100
1.8-1.820.24031310.19552706X-RAY DIFFRACTION100
1.82-1.850.24521150.19292725X-RAY DIFFRACTION100
1.85-1.880.21771280.20372729X-RAY DIFFRACTION100
1.88-1.910.24061370.20432704X-RAY DIFFRACTION100
1.91-1.940.19861570.18462692X-RAY DIFFRACTION100
1.94-1.980.20981320.17082725X-RAY DIFFRACTION100
1.98-2.020.19721430.16712678X-RAY DIFFRACTION100
2.02-2.060.21421530.16552731X-RAY DIFFRACTION100
2.06-2.10.20111420.16452693X-RAY DIFFRACTION100
2.1-2.150.20921360.16012711X-RAY DIFFRACTION100
2.15-2.20.19721520.16042714X-RAY DIFFRACTION100
2.2-2.260.20771530.16622717X-RAY DIFFRACTION100
2.26-2.330.18311430.16172707X-RAY DIFFRACTION100
2.33-2.410.20491430.1652715X-RAY DIFFRACTION100
2.41-2.490.20451110.17442735X-RAY DIFFRACTION100
2.49-2.590.18641560.17372718X-RAY DIFFRACTION100
2.59-2.710.19191280.18162731X-RAY DIFFRACTION100
2.71-2.850.18671540.17122709X-RAY DIFFRACTION100
2.85-3.030.19231290.17292767X-RAY DIFFRACTION100
3.03-3.270.19891570.16832686X-RAY DIFFRACTION100
3.27-3.590.17231550.15832763X-RAY DIFFRACTION100
3.59-4.110.14881410.1422732X-RAY DIFFRACTION100
4.11-5.180.13051780.12442728X-RAY DIFFRACTION100
5.18-47.850.18821340.17452853X-RAY DIFFRACTION100

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