[English] 日本語
Yorodumi- PDB-4s1j: Crystal structure of cyclophilin mutant V33A from Leishmania dono... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4s1j | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of cyclophilin mutant V33A from Leishmania donovani at 2.3 angstrom. | ||||||
Components | Peptidyl-prolyl cis-trans isomeraseProlyl isomerase | ||||||
Keywords | ISOMERASE / Rotamase / peptidyl-prolyl cis-trans isomerase / Cytosol | ||||||
Function / homology | Function and homology information peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding Similarity search - Function | ||||||
Biological species | Leishmania donovani (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Roy, S. / Datta, A.K. / Banerjee, R. | ||||||
Citation | Journal: To be Published Title: Characterization and prediction of thermal stability of cyclophilin mutants from L.donovani Authors: Roy, S. / Datta, A.K. / Banerjee, R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4s1j.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4s1j.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 4s1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s1/4s1j ftp://data.pdbj.org/pub/pdb/validation_reports/s1/4s1j | HTTPS FTP |
---|
-Related structure data
Related structure data | 4s1eC 2haqS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19046.553 Da / Num. of mol.: 2 / Fragment: Cyclophilin, peptidyl-prolyl cis-trans-isomerase / Mutation: V33A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania donovani (eukaryote) / Strain: BPK282A1 / Gene: CYP, LDBPK_060120 / Plasmid: pQE32 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: E9B8M3, peptidylprolyl isomerase #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 43.97 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 10% PEG3350, 0.02 M Tris-HCl, 0.02% azide, 7 mg/mL protein, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å | |||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 23, 2011 | |||||||||||||||||||||
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||
Reflection | Resolution: 2.3→48.53 Å / Num. all: 14471 / Num. obs: 14068 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 36.4 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.8 | |||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2HAQ Resolution: 2.3→48.5 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.83 Å2
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.5 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|