[English] 日本語
Yorodumi- PDB-6i39: Crystal structure of v31Pizza6-AYW, a circularly permuted designe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6i39 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of v31Pizza6-AYW, a circularly permuted designer protein | ||||||||||||
Components | v31Pizza6-AYW | ||||||||||||
Keywords | DE NOVO PROTEIN / circularly permuted designer protein / artificial protein / beta-propeller / Pizza | ||||||||||||
Biological species | synthetic construct (others) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å | ||||||||||||
Authors | Mylemans, B. / Noguchi, H. / Deridder, E. / Voet, A.R.D. | ||||||||||||
Funding support | Belgium, 3items
| ||||||||||||
Citation | Journal: Protein Sci. / Year: 2020 Title: Influence of circular permutations on the structure and stability of a six-fold circular symmetric designer protein. Authors: Mylemans, B. / Noguchi, H. / Deridder, E. / Lescrinier, E. / Tame, J.R.H. / Voet, A.R.D. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6i39.cif.gz | 122.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6i39.ent.gz | 94.1 KB | Display | PDB format |
PDBx/mmJSON format | 6i39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i3/6i39 ftp://data.pdbj.org/pub/pdb/validation_reports/i3/6i39 | HTTPS FTP |
---|
-Related structure data
Related structure data | 6i37C 6i38C 6i3aC 6i3bC 6f0qS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 25786.428 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21 (bacteria) |
---|---|
#2: Chemical | ChemComp-MG / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.84 % |
---|---|
Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop Details: 0.1 Magnesium Chloride 16%(w/v) Tris-HCl pH8.5 +20% Glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.05→49.464 Å / Num. obs: 98363 / % possible obs: 99.9 % / Redundancy: 23.4 % / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.05→1.07 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6F0Q Resolution: 1.05→49.464 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.52
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.05→49.464 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|