[English] 日本語
![](img/lk-miru.gif)
- PDB-6cd2: Crystal structure of the PapC usher bound to the chaperone-adhesi... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6cd2 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the PapC usher bound to the chaperone-adhesin PapD-PapG | ||||||||||||
![]() |
| ||||||||||||
![]() | MEMBRANE PROTEIN/CHAPERONE / outer membrane usher / P pilus assembly / usher activation / MEMBRANE PROTEIN / MEMBRANE PROTEIN-CHAPERONE complex | ||||||||||||
Function / homology | ![]() fimbrial usher porin activity / pilus assembly / pilus / chaperone-mediated protein folding / cell outer membrane / cell wall organization / outer membrane-bounded periplasmic space / carbohydrate binding / cell adhesion / extracellular region / identical protein binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Omattage, N.S. / Deng, Z. / Yuan, P. / Hultgren, S.J. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Structural basis for usher activation and intramolecular subunit transfer in P pilus biogenesis in Escherichia coli. Authors: Omattage, N.S. / Deng, Z. / Pinkner, J.S. / Dodson, K.W. / Almqvist, F. / Yuan, P. / Hultgren, S.J. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 462.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 380.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 455.3 KB | Display | |
Data in XML | ![]() | 41.5 KB | Display | |
Data in CIF | ![]() | 57.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 25031.303 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Protein | Mass: 35519.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
#3: Protein | Mass: 80472.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
Sequence details | The poly-UNK fragments in PapC sequence represent portions that the residue identities cannot be ...The poly-UNK fragments in PapC sequence represent portions that the residue identities cannot be determined from electron density. The full sequence of the entity is VEFNTDVLDA |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 5.12 Å3/Da / Density % sol: 75.99 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 50 mM sodium citrate pH 5.0-6.0, 50 mM lithium sulfate, 50 mM sodium sulfate and 7-14% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 27152 / % possible obs: 98.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.054 / Rrim(I) all: 0.134 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 3.7→3.83 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3048 / Rpim(I) all: 0.448 / % possible all: 92.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 2VQI, 2WMP, 1J8S, 3L48 Resolution: 3.7→50.01 Å / Cor.coef. Fo:Fc: 0.832 / Cor.coef. Fo:Fc free: 0.791 / SU B: 91.949 / SU ML: 0.615 / Cross valid method: THROUGHOUT / ESU R Free: 0.77 / 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: 135.172 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.7→50.01 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|