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- PDB-7wvh: Structure of NAD+ glycohydrolase/Streptolysin O complex from Grou... -

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Basic information

Entry
Database: PDB / ID: 7wvh
TitleStructure of NAD+ glycohydrolase/Streptolysin O complex from Group A streptococcus
Components
  • NAD+-glycohydrolase
  • Streptolysin O
KeywordsTOXIN / Group A streptococcus / toxins / protein complex / SLO / NADase
Function / homology
Function and homology information


cholesterol binding / toxin activity / killing of cells of another organism / hydrolase activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Nicotine adenine dinucleotide glycohydrolase / NAD glycohydrolase, helical linker domain / NAD glycohydrolase catalytic domain / Thiol-activated cytolysins signature. / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin
Similarity search - Domain/homology
NAD+-glycohydrolase / Streptolysin O
Similarity search - Component
Biological speciesStreptococcus pyogenes A20 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsTsai, W.-J. / Wang, S.-Y.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)MOST 109-2320-B-006-066 Taiwan
CitationJournal: Commun Biol / Year: 2023
Title: Structural basis underlying the synergism of NADase and SLO during group A Streptococcus infection.
Authors: Tsai, W.J. / Lai, Y.H. / Shi, Y.A. / Hammel, M. / Duff, A.P. / Whitten, A.E. / Wilde, K.L. / Wu, C.M. / Knott, R. / Jeng, U.S. / Kang, C.Y. / Hsu, C.Y. / Wu, J.L. / Tsai, P.J. / Chiang-Ni, C. ...Authors: Tsai, W.J. / Lai, Y.H. / Shi, Y.A. / Hammel, M. / Duff, A.P. / Whitten, A.E. / Wilde, K.L. / Wu, C.M. / Knott, R. / Jeng, U.S. / Kang, C.Y. / Hsu, C.Y. / Wu, J.L. / Tsai, P.J. / Chiang-Ni, C. / Wu, J.J. / Lin, Y.S. / Liu, C.C. / Senda, T. / Wang, S.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD+-glycohydrolase
D: Streptolysin O
C: Streptolysin O
B: NAD+-glycohydrolase


Theoretical massNumber of molelcules
Total (without water)167,4544
Polymers167,4544
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, SEC-SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)246.094, 52.477, 169.397
Angle α, β, γ (deg.)90.00, 132.04, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NAD+-glycohydrolase


Mass: 30953.066 Da / Num. of mol.: 2 / Mutation: G330D, G368R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes A20 (bacteria) / Gene: spn / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: D7S0C0
#2: Protein Streptolysin O / SLO / Thiol-activated cytolysin


Mass: 52774.035 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes A20 (bacteria) / Gene: slo, SPy_0167, M5005_Spy0141 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0C0I3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.3 / Details: 17.5% PEG 3350, 100mM HEPES / PH range: 6.9-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 55058 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.025 / Rrim(I) all: 0.048 / Χ2: 0.926 / Net I/σ(I): 17.3
Reflection shellResolution: 2.45→2.49 Å / Num. unique obs: 985 / CC1/2: 0.874

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KT6, 4HSC

4kt6

4hsc


Resolution: 2.45→26.12 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2645 2836 5.15 %
Rwork0.2131 --
obs0.2158 55058 92.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→26.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10978 0 0 326 11304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111162
X-RAY DIFFRACTIONf_angle_d1.20415037
X-RAY DIFFRACTIONf_dihedral_angle_d15.2931460
X-RAY DIFFRACTIONf_chiral_restr0.0621676
X-RAY DIFFRACTIONf_plane_restr0.0081911
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.490.2937750.2621212X-RAY DIFFRACTION43
2.49-2.540.3396760.26481606X-RAY DIFFRACTION57
2.54-2.590.27611230.25151928X-RAY DIFFRACTION70
2.59-2.640.30291410.24882336X-RAY DIFFRACTION83
2.64-2.70.29461150.26632623X-RAY DIFFRACTION93
2.7-2.760.34291480.27642830X-RAY DIFFRACTION99
2.76-2.830.30041290.27292754X-RAY DIFFRACTION100
2.83-2.910.31461180.26032901X-RAY DIFFRACTION100
2.91-2.990.32431400.26212798X-RAY DIFFRACTION100
2.99-3.090.27561580.24162833X-RAY DIFFRACTION100
3.09-3.20.31931570.24732763X-RAY DIFFRACTION100
3.2-3.330.26832080.24152819X-RAY DIFFRACTION100
3.33-3.480.26441550.22522799X-RAY DIFFRACTION100
3.48-3.660.29221770.21452786X-RAY DIFFRACTION100
3.66-3.890.29441620.19862829X-RAY DIFFRACTION100
3.89-4.190.23011450.19152842X-RAY DIFFRACTION100
4.19-4.610.20421340.16772868X-RAY DIFFRACTION100
4.61-5.270.21951590.16882899X-RAY DIFFRACTION100
5.27-6.620.24091840.1992845X-RAY DIFFRACTION100
6.62-26.120.22791320.17742951X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 31.647 Å / Origin y: -11.7148 Å / Origin z: 32.2377 Å
111213212223313233
T0.315 Å2-0.0228 Å20.0079 Å2-0.2294 Å2-0.0171 Å2--0.2735 Å2
L1.4259 °20.0484 °20.0993 °2-0.03 °2-0.0401 °2--0.1095 °2
S-0.0781 Å °0.4587 Å °-0.0185 Å °-0.0426 Å °0.055 Å °-0.0075 Å °0.0008 Å °0.0312 Å °0.0195 Å °
Refinement TLS groupSelection details: all

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