[English] 日本語
![](img/lk-miru.gif)
- PDB-5i1n: Villin headpiece subdomain with a Gln26 to beta-3-homoglutamine s... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5i1n | |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Villin headpiece subdomain with a Gln26 to beta-3-homoglutamine substitution | |||||||||||||||
![]() |
| |||||||||||||||
![]() | DE NOVO PROTEIN / quasiracemic / foldamer / alpha/beta peptide | |||||||||||||||
Function / homology | ![]() regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization ...regulation of actin nucleation / cytoplasmic actin-based contraction involved in cell motility / lysophosphatidic acid binding / regulation of lamellipodium morphogenesis / filopodium tip / positive regulation of actin filament bundle assembly / actin filament severing / regulation of wound healing / actin filament capping / actin filament depolymerization / barbed-end actin filament capping / actin polymerization or depolymerization / cellular response to hepatocyte growth factor stimulus / positive regulation of epithelial cell migration / actin filament bundle / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / microvillus / cellular response to epidermal growth factor stimulus / ruffle / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / filopodium / response to bacterium / epidermal growth factor receptor signaling pathway / actin filament binding / actin cytoskeleton / lamellipodium / regulation of cell shape / positive regulation of cell migration / calcium ion binding / protein homodimerization activity / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() synthetic construct (others) | |||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||
![]() | Kreitler, D.F. / Mortenson, D.E. / Gellman, S.H. / Forest, K.T. | |||||||||||||||
Funding support | ![]()
| |||||||||||||||
![]() | ![]() Title: Effects of Single alpha-to-beta Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization. Authors: Kreitler, D.F. / Mortenson, D.E. / Forest, K.T. / Gellman, S.H. | |||||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 184 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 161.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 488.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 491.9 KB | Display | |
Data in XML | ![]() | 15.3 KB | Display | |
Data in CIF | ![]() | 22.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5i1oC ![]() 5i1pC ![]() 5i1sC ![]() 3tryS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein/peptide | Mass: 4102.778 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide, fmoc solid phase synthesis / Source: (synth.) ![]() ![]() #2: Polypeptide(D) | Mass: 4083.716 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: synthetic peptide, fmoc solid phase synthesis / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 34 % / Description: plate-like |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate pH 4.6, 1.5 M ammonium sulfate, 30% (v/v) PEG2000MME |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 16, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.3→36.92 Å / Num. obs: 53932 / % possible obs: 92.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.591 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.09 / Χ2: 0.989 / Net I/σ(I): 8.73 / Num. measured all: 210950 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
|
-
Processing
Software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3try Resolution: 1.3→36.92 Å / Rfactor Rfree: 0.231 / Rfactor Rwork: 0.206 / Cross valid method: FREE R-VALUE | |||||||||||||||||||||
Displacement parameters | Biso max: 107.37 Å2 / Biso mean: 25.1688 Å2 / Biso min: 7.89 Å2 | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→36.92 Å
|