[English] 日本語
![](img/lk-miru.gif)
- PDB-5hdl: Crystal structure of shaft pilin spaA from Lactobacillus rhamnosu... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5hdl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of shaft pilin spaA from Lactobacillus rhamnosus GG - E269A mutant | ||||||
![]() | Cell surface protein SpaA![]() | ||||||
![]() | ![]() ![]() ![]() ![]() | ||||||
Function / homology | ![]() Gram-positive pilin subunit D1, N-terminal / Gram-positive pilin subunit D1, N-terminal domain / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / ![]() ![]() ![]() ![]() ![]() Similarity search - Domain/homology | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: New insights about pilus formation in gut-adapted Lactobacillus rhamnosus GG from the crystal structure of the SpaA backbone-pilin subunit Authors: Chaurasia, P. / Pratap, S. / von Ossowski, I. / Palva, A. / Krishnan, V. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 315.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 258.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5f44SC ![]() 5faaC ![]() 5fgrC ![]() 5fgsC ![]() 5fieC ![]() 5hbbC ![]() 5htsC ![]() 5j4mC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
3 | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 0 / Auth seq-ID: 38 - 302 / Label seq-ID: 11 - 275
NCS ensembles :
|
-
Components
#1: Protein | ![]() Mass: 30665.463 Da / Num. of mol.: 3 / Fragment: UNP residues 35-302 / Mutation: E269A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Water | ChemComp-HOH / | ![]() |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.09 Å3/Da / Density % sol: 69.93 % |
---|---|
Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: 0.2 M tri-Potassium citrate, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 23, 2015 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.39→80.79 Å / Num. obs: 59176 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.39→2.67 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.9 / % possible all: 99.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5F44 Resolution: 2.39→80.79 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.942 / SU B: 18.427 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.394 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.39→80.79 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|