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Yorodumi- PDB-7wvh: Structure of NAD+ glycohydrolase/Streptolysin O complex from Grou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wvh | ||||||
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Title | Structure of NAD+ glycohydrolase/Streptolysin O complex from Group A streptococcus | ||||||
Components |
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Keywords | TOXIN / 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 | ||||||
Biological species | Streptococcus pyogenes A20 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å | ||||||
Authors | Tsai, W.-J. / Wang, S.-Y. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wvh.cif.gz | 566.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wvh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7wvh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wvh_validation.pdf.gz | 470.3 KB | Display | wwPDB validaton report |
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Full document | 7wvh_full_validation.pdf.gz | 498.9 KB | Display | |
Data in XML | 7wvh_validation.xml.gz | 54.4 KB | Display | |
Data in CIF | 7wvh_validation.cif.gz | 76 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wv/7wvh ftp://data.pdbj.org/pub/pdb/validation_reports/wv/7wvh | HTTPS FTP |
-Related structure data
Related structure data | 4hscS 4kt6S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.29 % |
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Crystal grow | Temperature: 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
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.45→2.49 Å / Num. unique obs: 985 / CC1/2: 0.874 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→26.12 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 31.647 Å / Origin y: -11.7148 Å / Origin z: 32.2377 Å
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Refinement TLS group | Selection details: all |