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Yorodumi- PDB-8f70: Identification of an Immunodominant region on a Group A Streptoco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f70 | ||||||
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Title | Identification of an Immunodominant region on a Group A Streptococcus T-antigen Reveals Temperature-Dependent Motion in Pili | ||||||
Components | T18.1 Major pilin backbone protein T-antigen,Major pilin backbone protein T-antigen | ||||||
Keywords | STRUCTURAL PROTEIN / Streptococcus T-antigen major pilin backbone protein | ||||||
Function / homology | Streptococcal pilin isopeptide linker / Streptococcal pilin isopeptide linker superfamily / Spy0128-like isopeptide containing domain / Domain of unknown function DUF5979 / Domain of unknown function (DUF5979) / metal ion binding / Major pilin backbone protein T-antigen Function and homology information | ||||||
Biological species | Streptococcus pyogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||
Authors | Young, P.G. / Moreland, N.J. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: Virulence / Year: 2023 Title: Identification of an immunodominant region on a group A Streptococcus T-antigen reveals temperature-dependent motion in pili. Authors: Raynes, J.M. / Young, P.G. / Lorenz, N. / Loh, J.M.S. / McGregor, R. / Baker, E.N. / Proft, T. / Moreland, N.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8f70.cif.gz | 129.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f70.ent.gz | 96.5 KB | Display | PDB format |
PDBx/mmJSON format | 8f70.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f70_validation.pdf.gz | 420.4 KB | Display | wwPDB validaton report |
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Full document | 8f70_full_validation.pdf.gz | 422 KB | Display | |
Data in XML | 8f70_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 8f70_validation.cif.gz | 32.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f7/8f70 ftp://data.pdbj.org/pub/pdb/validation_reports/f7/8f70 | HTTPS FTP |
-Related structure data
Related structure data | 8f5nC 6n0aS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 62326.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: tee / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / References: UniProt: A0A096ZH83 | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.12M 1,6-Hexanediol, 0.12M 1-Butanol, 0.12M 1,2-Propanediol, 0.12M 2-Propanol, 0.12M 1,4-Butanediol, 0.12M 1,3-Propanediol, 0.1M Sodium HEPES, 0.1M MOPS (acid), 20% v/v Ethylene glycol, 10 % w/v PEG 8000 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95374 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95374 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→47.58 Å / Num. obs: 27529 / % possible obs: 99.4 % / Redundancy: 5.3 % / CC1/2: 0.993 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.071 / Rrim(I) all: 0.17 / Χ2: 0.94 / Net I/σ(I): 7.2 / Num. measured all: 145410 |
Reflection shell | Resolution: 2.29→2.37 Å / % possible obs: 95 % / Redundancy: 5.2 % / Rmerge(I) obs: 1.09 / Num. measured all: 13215 / Num. unique obs: 2540 / CC1/2: 0.714 / Rpim(I) all: 0.506 / Rrim(I) all: 1.206 / Χ2: 1 / Net I/σ(I) obs: 1.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N0A Resolution: 2.29→47.58 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.434 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.739 Å2
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Refinement step | Cycle: 1 / Resolution: 2.29→47.58 Å
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Refine LS restraints |
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