+Open data
-Basic information
Entry | Database: PDB / ID: 8bk4 | ||||||
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Title | Full length structure of the apo-state LpMIP. | ||||||
Components | Macrophage infectivity potentiator | ||||||
Keywords | STRUCTURAL PROTEIN / Macrophage / potentiator / soluble / protein. | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / chromatin / nucleolus / extracellular region Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Whittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bk4.cif.gz | 82.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bk4.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bk4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bk4_validation.pdf.gz | 879.2 KB | Display | wwPDB validaton report |
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Full document | 8bk4_full_validation.pdf.gz | 879.7 KB | Display | |
Data in XML | 8bk4_validation.xml.gz | 9.9 KB | Display | |
Data in CIF | 8bk4_validation.cif.gz | 13.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/8bk4 ftp://data.pdbj.org/pub/pdb/validation_reports/bk/8bk4 | HTTPS FTP |
-Related structure data
Related structure data | 8bjcC 8bjdC 8bjeC 8bk5C 8bk6C 1jvwS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 18472.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: MIP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q09734, peptidylprolyl isomerase |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-WRL / ( |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 30 %(v/v) MPD, 0.2 M ammonium acetate, 0.1 M sodium citrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å |
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: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→43.84 Å / Num. obs: 28364 / % possible obs: 74.79 % / Redundancy: 8.5 % / Rrim(I) all: 0.08 / Net I/σ(I): 15.56 |
Reflection shell | Resolution: 1.342→1.39 Å / Num. unique obs: 209 / Rrim(I) all: 0.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JVW Resolution: 1.34→43.83 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 1.34→43.83 Å
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