[English] 日本語
![](img/lk-miru.gif)
- PDB-8f70: Identification of an Immunodominant region on a Group A Streptoco... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8f70 | ||||||
---|---|---|---|---|---|---|---|
Title | Identification of an Immunodominant region on a Group A Streptococcus T-antigen Reveals Temperature-Dependent Motion in Pili | ||||||
![]() | T18.1 Major pilin backbone protein T-antigen,Major pilin backbone protein T-antigen | ||||||
![]() | 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![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Young, P.G. / Moreland, N.J. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 129.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 96.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 420.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 422 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f5nC ![]() 6n0aS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 62326.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.87 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.29→47.58 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|