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- PDB-6u3u: Crystal Structure of Shiga Toxin 2K -

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Basic information

Entry
Database: PDB / ID: 6u3u
TitleCrystal Structure of Shiga Toxin 2K
Components(Shiga toxin 2K subunit ...) x 2
KeywordsTOXIN / Shiga Toxin / AB5 Toxin / Toxoid
Function / homology
Function and homology information


hemolysis by symbiont of host erythrocytes / rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / extracellular region / metal ion binding
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
rRNA N-glycosylase / Shiga toxin 2B subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.287 Å
AuthorsZhang, Y.Z. / He, X.H.
Funding support United States, 1items
OrganizationGrant numberCountry
United States Department of Agriculture (USDA) United States
CitationJournal: Microorganisms / Year: 2019
Title: Structural and Functional Characterization of Stx2k, a New Subtype of Shiga Toxin 2.
Authors: Hughes, A.C. / Zhang, Y. / Bai, X. / Xiong, Y. / Wang, Y. / Yang, X. / Xu, Q. / He, X.
History
DepositionAug 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_symmetry
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
B: Shiga toxin 2K subunit A
C: Shiga toxin 2K subunit B
D: Shiga toxin 2K subunit B
E: Shiga toxin 2K subunit B
H: Shiga toxin 2K subunit B
I: Shiga toxin 2K subunit B
A: Shiga toxin 2K subunit A
F: Shiga toxin 2K subunit B
G: Shiga toxin 2K subunit B
J: Shiga toxin 2K subunit B
K: Shiga toxin 2K subunit B
L: Shiga toxin 2K subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,54022
Polymers143,56412
Non-polymers97610
Water2,090116
1
B: Shiga toxin 2K subunit A
C: Shiga toxin 2K subunit B
D: Shiga toxin 2K subunit B
E: Shiga toxin 2K subunit B
H: Shiga toxin 2K subunit B
I: Shiga toxin 2K subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,39313
Polymers71,7826
Non-polymers6117
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-16 kcal/mol
Surface area23200 Å2
MethodPISA
2
A: Shiga toxin 2K subunit A
F: Shiga toxin 2K subunit B
G: Shiga toxin 2K subunit B
J: Shiga toxin 2K subunit B
K: Shiga toxin 2K subunit B
L: Shiga toxin 2K subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1489
Polymers71,7826
Non-polymers3663
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-21 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.178, 157.022, 107.407
Angle α, β, γ (deg.)90.000, 94.610, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Shiga toxin 2K subunit ... , 2 types, 12 molecules BACDEHIFGJKL

#1: Protein Shiga toxin 2K subunit A


Mass: 33038.961 Da / Num. of mol.: 2 / Mutation: E167Q
Source method: isolated from a genetically manipulated source
Details: E167Q / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: stx2A / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle T7 / References: UniProt: L0I969
#2: Protein
Shiga toxin 2K subunit B / Shiga toxin 2B subunit / Verocytotoxin 2 B-subunit


Mass: 7748.584 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: vtx2B, stx2B, stx2B_2, BvCmsKKP036_03423, BvCmsNSP045_04912
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q4PS70

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Non-polymers , 4 types, 126 molecules

#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 3.35 Å3/Da / Density % sol: 63.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, pH 7.5, 10% w/v PEG 8000, 15% Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.039→107.059 Å / Num. obs: 94159 / % possible obs: 93.6 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.027 / Rrim(I) all: 0.05 / Net I/σ(I): 13 / Num. measured all: 328715
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.039-2.1773.60.6611708447090.660.4050.7771.664.4
6.008-107.0593.50.0321631247070.9970.020.03830.298.4

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R4P

1r4p


Resolution: 2.287→52.076 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 26.91
RfactorNum. reflection% reflection
Rfree0.2245 1992 2.37 %
Rwork0.1968 --
obs0.1974 83973 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 191.64 Å2 / Biso mean: 75.3925 Å2 / Biso min: 39.69 Å2
Refinement stepCycle: final / Resolution: 2.287→52.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9873 0 135 116 10124
Biso mean--92.86 58.14 -
Num. residues----1266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2872-2.34440.31411440.2912581799
2.3444-2.40780.30841400.28125869100
2.4078-2.47870.29121480.2704587999
2.4787-2.55870.28861450.2671586499
2.5587-2.65010.25091310.2577585099
2.6501-2.75620.29471460.2501581098
2.7562-2.88160.30951350.2593582899
2.8816-3.03350.26411420.2537587599
3.0335-3.22360.28631580.2503587799
3.2236-3.47240.2421350.2391585699
3.4724-3.82180.24611340.2064583298
3.8218-4.37450.20451520.1645587799
4.3745-5.51050.171360.1483580498
5.5105-52.0760.1841460.1575594398

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