+
Open data
-
Basic information
Entry | Database: PDB / ID: 8bk6 | ||||||
---|---|---|---|---|---|---|---|
Title | A truncated structure of LpMIP with bound inhibitor JK095. | ||||||
![]() | Peptidyl-prolyl cis-trans isomerase | ||||||
![]() | STRUCTURAL PROTEIN / Macrophage / potentiator / soluble / protein. | ||||||
Function / homology | ![]() peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell outer membrane / protein folding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Whittaker, J.J. / Guskov, A. / Hellmich, A.U. / Goretzki, B. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Legionella pneumophila macrophage infectivity potentiator protein appendage domains modulate protein dynamics and inhibitor binding. Authors: Wiedemann, C. / Whittaker, J.J. / Perez Carrillo, V.H. / Goretzki, B. / Dajka, M. / Tebbe, F. / Harder, J.M. / Krajczy, P.R. / Joseph, B. / Hausch, F. / Guskov, A. / Hellmich, U.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 57.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 40.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 455.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 459.4 KB | Display | |
Data in XML | ![]() | 11.1 KB | Display | |
Data in CIF | ![]() | 13.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bjcC ![]() 8bjdC ![]() 8bjeC ![]() 8bk4C ![]() 8bk5C ![]() 1fd9S 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: 11942.639 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-MES / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.9 Å3/Da / Density % sol: 57.64 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 20 %(v/v) 2-propanol, 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.263→59.92 Å / Num. obs: 13801 / % possible obs: 99.63 % / Redundancy: 7.5 % / Rrim(I) all: 0.06 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.263→5.5 Å / Num. unique obs: 1334 / Rrim(I) all: 0.09 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1FD9 Resolution: 2.263→59.92 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 2.263 / Phase error: 36.19 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.263→59.92 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|