[English] 日本語
![](img/lk-miru.gif)
- PDB-6g8e: Crystal Structure of the Amyloid-like VTQVGF segment from the R5 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6g8e | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the Amyloid-like VTQVGF segment from the R5 repeat of the E. coli Biofilm-associated CsgA Curli protein | ||||||
![]() | Major curlin subunit | ||||||
![]() | PROTEIN FIBRIL / Bacterial steric-zipper cross-beta amyloid fibril from E. coli | ||||||
Function / homology | Curlin associated / Curlin associated repeat / regulation of amyloid fibril formation / single-species biofilm formation / pilus / amyloid fibril formation / cell adhesion / identical protein binding / Major curlin subunit![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
Model details | Curli | ||||||
![]() | Landau, M. / Perov, S. | ||||||
![]() | ![]() Title: Structural Insights into Curli CsgA Cross-beta Fibril Architecture Inspire Repurposing of Anti-amyloid Compounds as Anti-biofilm Agents. Authors: Perov, S. / Lidor, O. / Salinas, N. / Golan, N. / Tayeb-Fligelman, E. / Deshmukh, M. / Willbold, D. / Landau, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 11.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 5.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 371.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 371.6 KB | Display | |
Data in XML | ![]() | 2.7 KB | Display | |
Data in CIF | ![]() | 2.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 649.735 Da / Num. of mol.: 2 Fragment: Amyloid spine segment VTQVGF from CsgA (residues 137-142) secreted by E. coli Source method: obtained synthetically / Details: VTQVGF from CsgA, synthesized / Source: (synth.) ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.42 Å3/Da / Density % sol: 13.14 % / Description: Needle-like |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Reservoir contained 3.0 M Sodium chloride and 0.1 M BIS-Tris pH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 6, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→19.93 Å / Num. obs: 776 / % possible obs: 98.4 % / Redundancy: 6.923 % / Biso Wilson estimate: 16.637 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.275 / Rrim(I) all: 0.298 / Χ2: 0.849 / Net I/σ(I): 5.02 / Num. measured all: 5372 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR | Model details: Phaser MODE: MR_AUTO / Packing: 0
|
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: Ideal beta-strand Resolution: 1.7→19.93 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.981 / SU B: 1.896 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.087 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.21 Å2 / Biso mean: 9.47 Å2 / Biso min: 6.37 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.7→19.93 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|