[English] 日本語
![](img/lk-miru.gif)
- PDB-5e7b: Structure of a nanobody (vHH) from camel against phage Tuc2009 RB... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5e7b | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a nanobody (vHH) from camel against phage Tuc2009 RBP (BppL, ORF53) | ||||||
![]() | nanobody nano-L06 | ||||||
![]() | IMMUNE SYSTEM / bacteriophages / Lactococcus lactis / receptor binding protein / single-chain nanobody | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. ...Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C. | ||||||
![]() | ![]() Title: The Atomic Structure of the Phage Tuc2009 Baseplate Tripod Suggests that Host Recognition Involves Two Different Carbohydrate Binding Modules. Authors: Legrand, P. / Collins, B. / Blangy, S. / Murphy, J. / Spinelli, S. / Gutierrez, C. / Richet, N. / Kellenberger, C. / Desmyter, A. / Mahony, J. / van Sinderen, D. / Cambillau, C. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 90.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 74.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 419.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 420.2 KB | Display | |
Data in XML | ![]() | 9 KB | Display | |
Data in CIF | ![]() | 13 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-
Components
#1: Antibody | Mass: 14164.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: obtained upon immunization / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: mixing 100-300 nl of 12 mg.mL-1 protein (Na2HPO4, 10 mM; KH2PO4, 1.8 mM, pH7.4; NaCl, 137 mM; KCl, 2.7mM) with 100 nl precipitant solution in 25-30 % PEG4000, 0.2 M Imidazole (pH 6.0). PH range: 7.2 - 7.4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.86 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→45.1 Å / Num. all: 51977 / Num. obs: 52014 / % possible obs: 96.6 % / Redundancy: 19.5 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.1→1.13 Å / Redundancy: 19.2 % / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 1.5 / % possible all: 91.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→14.97 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|