[English] 日本語
![](img/lk-miru.gif)
- PDB-6atu: Exploring Cystine Dense Peptide Space to Open a Unique Molecular ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6atu | ||||||
---|---|---|---|---|---|---|---|
Title | Exploring Cystine Dense Peptide Space to Open a Unique Molecular Toolbox | ||||||
![]() | Elafin | ||||||
![]() | TOXIN / Knottins / Cystine knot / Toxins | ||||||
Function / homology | ![]() structural constituent of skin epidermis / copulation / Formation of the cornified envelope / peptide cross-linking / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity / antibacterial humoral response ...structural constituent of skin epidermis / copulation / Formation of the cornified envelope / peptide cross-linking / cornified envelope / Antimicrobial peptides / endopeptidase inhibitor activity / extracellular matrix / serine-type endopeptidase inhibitor activity / antibacterial humoral response / innate immune response / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gewe, M.M. / Rupert, P. / Strong, R.K. | ||||||
![]() | ![]() Title: Screening, large-scale production and structure-based classification of cystine-dense peptides. Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S. ...Authors: Correnti, C.E. / Gewe, M.M. / Mehlin, C. / Bandaranayake, A.D. / Johnsen, W.A. / Rupert, P.B. / Brusniak, M.Y. / Clarke, M. / Burke, S.E. / De Van Der Schueren, W. / Pilat, K. / Turnbaugh, S.M. / May, D. / Watson, A. / Chan, M.K. / Bahl, C.D. / Olson, J.M. / Strong, R.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 173.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 140.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 529.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 531.6 KB | Display | |
Data in XML | ![]() | 31.6 KB | Display | |
Data in CIF | ![]() | 47 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6atlC ![]() 6atnC ![]() 6atsC ![]() 6atwC ![]() 6au7C ![]() 6aupC ![]() 6av8C ![]() 6avaC ![]() 6avcC ![]() 6avdC ![]() 1fleS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
-
Components
#1: Protein | Mass: 6158.354 Da / Num. of mol.: 18 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.4M Na malonate pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→71.33 Å / Num. obs: 41565 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.028 / Net I/σ(I): 29.91 |
Reflection shell | Resolution: 2.4→2.44 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.491 / Num. unique obs: 2035 / CC1/2: 0.94 / Rpim(I) all: 0.196 / % possible all: 97.2 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 1FLE Resolution: 2.4→71.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 8.379 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.249 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.584 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.4→71.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|