+Open data
-Basic information
Entry | Database: PDB / ID: 8p3d | ||||||
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Title | Full length structure of TcMIP with bound inhibitor NJS224. | ||||||
Components | peptidylprolyl isomerase | ||||||
Keywords | STRUCTURAL PROTEIN / Macrophage / potentiator / soluble / protein | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / chromatin / nucleolus Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Whittaker, J.J. / Guskov, A. / Goretzki, B. / Hellmich, U.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Structural dynamics of macrophage infectivity potentiator proteins (MIPs) are differentially modulated by inhibitors and appendage domains Authors: Whittaker, J.J. / Guskov, A. / Goretzki, B. / 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 | 8p3d.cif.gz | 80.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8p3d.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 8p3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8p3d_validation.pdf.gz | 752.2 KB | Display | wwPDB validaton report |
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Full document | 8p3d_full_validation.pdf.gz | 752.3 KB | Display | |
Data in XML | 8p3d_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 8p3d_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/8p3d ftp://data.pdbj.org/pub/pdb/validation_reports/p3/8p3d | HTTPS FTP |
-Related structure data
Related structure data | 8p3cC 8p42C 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: 18401.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: Tc00.1047053508897.110 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4D932, peptidylprolyl isomerase | ||||
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#2: Chemical | ChemComp-WS5 / ( Mass: 504.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H33FN4O4S | ||||
#3: Chemical | ChemComp-NA / #4: 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: 2.34 Å3/Da / Density % sol: 47.44 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 5 mM Tris pH 7.5 150 mM NaCl PEG2000 12 % |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→46.77 Å / Num. obs: 18060 / % possible obs: 96.58 % / Redundancy: 7.7 % / CC1/2: 0.91 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 1.71→1.77 Å / Num. unique obs: 1811 / CC1/2: 0.78 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→46.77 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6 / 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: 1.71→46.77 Å
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Refine LS restraints |
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LS refinement shell |
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