[English] 日本語
![](img/lk-miru.gif)
- PDB-5n8w: CRYSTAL STRUCTURE OF STREPTAVIDIN with D-amino acid containing pe... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5n8w | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF STREPTAVIDIN with D-amino acid containing peptide GGwhdeatwkpG | ||||||
![]() |
| ||||||
![]() | biotin binding protein / STREPTAVIDIN / BIOTIN BINDING / D-AMINO ACIDS / STREPTAVIDIN PEPTIDE COMPLEX / STREPTAVIDIN PEPTIDE 11101 COMPLEX | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lyamichev, V. / Goodrich, L. / Sullivan, E. / Bannen, R. / Benz, J. / Albert, T. / Patel, J. | ||||||
![]() | ![]() Title: Stepwise Evolution Improves Identification of Diverse Peptides Binding to a Protein Target. Authors: Lyamichev, V.I. / Goodrich, L.E. / Sullivan, E.H. / Bannen, R.M. / Benz, J. / Albert, T.J. / Patel, J.J. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 129.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 107.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5n7xC ![]() 5n89C ![]() 5n8bC ![]() 5n8eC ![]() 5n8jC ![]() 5n8tC ![]() 5n99C C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18849.672 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Polypeptide(D) | Mass: 1617.739 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.3 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1M Magnesium acetate 0.1M MOPS pH 7.5 12% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→62.3 Å / Num. obs: 122566 / % possible obs: 99.2 % / Redundancy: 6.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.048 / Net I/σ(I): 17.4 |
Reflection shell | Resolution: 1.1→1.2 Å / Redundancy: 5.29 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 4.01 / Num. unique obs: 28666 / CC1/2: 0.792 / % possible all: 96.8 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.811 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.1→62.3 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|