[English] 日本語
Yorodumi
- PDB-7wvh: Structure of NAD+ glycohydrolase/Streptolysin O complex from Grou... -

+
Open data


ID or keywords:

Loading...

-
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


hemolysis in another organism / cholesterol binding / toxin activity / hydrolase activity / host cell plasma membrane / extracellular region / membrane
Similarity search - Function
Nicotine adenine dinucleotide glycohydrolase / NAD glycohydrolase, helical linker domain / Nicotine adenine dinucleotide glycohydrolase (NADase) / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more