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Yorodumi- PDB-8f5n: Identification of an Immunodominant region on a Group A Streptoco... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f5n | ||||||
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Title | Identification of an Immunodominant region on a Group A Streptococcus T-antigen Reveals Temperature-Dependent Motion in Pili | ||||||
Components |
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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) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Raynes, J.M. / 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 | 8f5n.cif.gz | 157 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8f5n.ent.gz | 118.9 KB | Display | PDB format |
PDBx/mmJSON format | 8f5n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8f5n_validation.pdf.gz | 894 KB | Display | wwPDB validaton report |
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Full document | 8f5n_full_validation.pdf.gz | 898 KB | Display | |
Data in XML | 8f5n_validation.xml.gz | 28.2 KB | Display | |
Data in CIF | 8f5n_validation.cif.gz | 41.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/8f5n ftp://data.pdbj.org/pub/pdb/validation_reports/f5/8f5n | HTTPS FTP |
-Related structure data
Related structure data | 8f70C 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: 31038.467 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M18 / Gene: tee 18.1 / Plasmid: pProExHta / Production host: Escherichia coli (E. coli) / References: UniProt: A0A096ZH83 |
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#2: Antibody | Mass: 23560.152 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pComb3X / Production host: Escherichia coli (E. coli) / Strain (production host): Top10F |
#3: Antibody | Mass: 23590.396 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pComb3X / Production host: Escherichia coli (E. coli) |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.95 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10% (w/v) PEG 8000, 20% (v/v) ethylene glycol, 0.3 Mdiethyleneglycol, 0.3 Mtriethyleneglycol, 0.3 M tetraethyleneglycol, 0.3 Mpentaethyleneglycol and 0.1 M MOPS/HEPES-Na pH 7.5 |
-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: 0.95372 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→41.87 Å / Num. obs: 65913 / % possible obs: 99.9 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.032 / Rrim(I) all: 0.084 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.425 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4228 / CC1/2: 0.769 / Rpim(I) all: 0.583 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6N0A Resolution: 1.9→41.9 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.804 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.141 / 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: 47.565 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→41.9 Å
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Refine LS restraints |
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