[English] 日本語
Yorodumi- PDB-3snv: Crystal structure of Symfoil-4T Permutation #1: de novo designed ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3snv | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Symfoil-4T Permutation #1: de novo designed beta-trefoil architecture with symmetric primary structure | ||||||
Components | Symfoil-4T/Permutation #1 synthetic protein | ||||||
Keywords | DE NOVO PROTEIN / beta-trefoil | ||||||
Function / homology | Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Blaber, M. / Longo, L. / Lee, J. | ||||||
Citation | Journal: To be Published Title: Folding pathway redundancy in symmetric protein architecture Authors: Longo, L. / Lee, J. / Blaber, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3snv.cif.gz | 63.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3snv.ent.gz | 46.6 KB | Display | PDB format |
PDBx/mmJSON format | 3snv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sn/3snv ftp://data.pdbj.org/pub/pdb/validation_reports/sn/3snv | HTTPS FTP |
---|
-Related structure data
Related structure data | 3o4bS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15994.363 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | THIS IS A CIRCULAR PERMUTATION OF THE SYMFOIL-4T PROTEIN (PDB ACCESSION 3O4B). IN THIS PERMUTATION ...THIS IS A CIRCULAR PERMUTATIO | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.57 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.9 M ammonium sulfate, 0.2 M lithium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Dec 19, 2010 / Details: Osmic confocal |
Radiation | Monochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→40 Å / Num. all: 13099 / Num. obs: 12051 / % possible obs: 92 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 4.64 / Num. unique all: 636 / % possible all: 57.9 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3O4B Resolution: 2.2→23.226 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7957 / SU ML: 0.39 / σ(F): 2 / Phase error: 27.35 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.747 Å2 / ksol: 0.377 e/Å3 | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 95.08 Å2 / Biso mean: 40.2462 Å2 / Biso min: 15.04 Å2
| |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→23.226 Å
| |||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4
|