[English] 日本語
Yorodumi- PDB-8os1: X-ray structure of the Peroxisomal Targeting Signal 1 (PTS1) of T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8os1 | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray structure of the Peroxisomal Targeting Signal 1 (PTS1) of Trypanosoma Cruzi PEX5 in complex with the PTS1 peptide | ||||||
Components |
| ||||||
Keywords | TRANSPORT PROTEIN / TPR domain / Complex / Peroxisomal targeting signal 1 binding domain / cargo recognition protein | ||||||
Function / homology | Function and homology information peroxisome matrix targeting signal-1 binding / protein import into peroxisome matrix, docking / peroxisomal membrane / cytosol Similarity search - Function | ||||||
Biological species | Trypanosoma cruzi (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Napolitano, V. / Blat, A. / Popowicz, G.M. / Dubin, G. | ||||||
Funding support | European Union, 1items
| ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Structural dynamics of the TPR domain of the peroxisomal cargo receptor Pex5 in Trypanosoma. Authors: Banasik, M. / Napolitano, V. / Blat, A. / Abdulkarim, K. / Plewka, J. / Czaplewski, C. / Gieldon, A. / Kozak, M. / Wladyka, B. / Popowicz, G. / Dubin, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8os1.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8os1.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 8os1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8os1_validation.pdf.gz | 503.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8os1_full_validation.pdf.gz | 511 KB | Display | |
Data in XML | 8os1_validation.xml.gz | 31.9 KB | Display | |
Data in CIF | 8os1_validation.cif.gz | 42.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/os/8os1 ftp://data.pdbj.org/pub/pdb/validation_reports/os/8os1 | HTTPS FTP |
-Related structure data
Related structure data | 9f8wC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein / Protein/peptide , 2 types, 4 molecules BADC
#1: Protein | Mass: 36216.625 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Gene: ECC02_006719 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7J6Y110 #2: Protein/peptide | Mass: 638.733 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Trypanosoma cruzi (eukaryote) |
---|
-Non-polymers , 6 types, 308 molecules
#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PEG / | #5: Chemical | #6: Chemical | ChemComp-MG / | #7: Chemical | ChemComp-TRS / | #8: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.73 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M MgCl2, 0.1 M Tris pH 8.5 and 30% (w/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→48.22 Å / Num. obs: 35080 / % possible obs: 95.9 % / Redundancy: 2.8 % / CC1/2: 0.959 / Net I/σ(I): 3.7 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 2248 / CC1/2: 0.539 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.22 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.898 / SU B: 7.096 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.271 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.849 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.1→48.22 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|