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Open data
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Basic information
Entry | Database: PDB / ID: 8bje | ||||||
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Title | A structure of the truncated LpMIP with bound inhibitor JK236. | ||||||
![]() | 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. / Goretzki, B. / Hellmich, U.A. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 70.3 KB | Display | ![]() |
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PDB format | ![]() | 49.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 929.1 KB | Display | ![]() |
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Full document | ![]() | 930 KB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 10.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8bjcC ![]() 8bjdC ![]() 8bk4C ![]() 8bk5C ![]() 8bk6C ![]() 1fd9S S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 14232.267 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-WRL / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.86 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 18 %(w/v) PEG 8000, 0.2 M zinc acetate, 0.1 M sodium cacodylate, pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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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: 1.44→45.86 Å / Num. obs: 23619 / % possible obs: 99.21 % / Redundancy: 10.5 % / Rrim(I) all: 0.07 / Net I/σ(I): 9.92 |
Reflection shell | Resolution: 1.44→1.49 Å / Num. unique obs: 2330 / Rrim(I) all: 0.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1FD9 Resolution: 1.49→45.86 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 36.27 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.49→45.86 Å
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Refine LS restraints |
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LS refinement shell |
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