[English] 日本語
![](img/lk-miru.gif)
- PDB-8fb6: Crystal structure of Ky15.10 Fab in complex with circumsporozoite... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8fb6 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Ky15.10 Fab in complex with circumsporozoite protein KQPA peptide | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / Malaria / Antibody | ||||||
Function / homology | ![]() entry into host cell by a symbiont-containing vacuole / external side of plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Prieto, K. / Thai, E. / Julien, J.P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Molecular determinants of cross-reactivity and potency by VH3-33 antibodies against the Plasmodium falciparum circumsporozoite protein. Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / ...Authors: Thai, E. / Murugan, R. / Binter, S. / Burn Aschner, C. / Prieto, K. / Kassardjian, A. / Obraztsova, A.S. / Kang, R.W. / Flores-Garcia, Y. / Mathis-Torres, S. / Li, K. / Horn, G.Q. / Huntwork, R.H.C. / Bolscher, J.M. / de Bruijni, M.H.C. / Sauerwein, R. / Dennison, S.M. / Tomaras, G.D. / Zavala, F. / Kellam, P. / Wardemann, H. / Julien, J.P. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 225.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 149.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 452.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 453.5 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8f95C ![]() 8f9eC ![]() 8f9fC ![]() 8f9sC ![]() 8f9tC ![]() 8f9uC ![]() 8f9vC ![]() 8f9wC ![]() 8fa6C ![]() 8fa7C ![]() 8fa8C ![]() 8fa9C ![]() 8fanC ![]() 8fasC ![]() 8fatC ![]() 8fb5C ![]() 8fb7C ![]() 8fb8C ![]() 8fbaC ![]() 8fdcC ![]() 8fddC C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 24547.369 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Antibody | Mass: 23534.154 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
#3: Protein/peptide | Mass: 1549.577 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) ![]() ![]() References: UniProt: P19597 | ||||
#4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.3 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M sodium acetate pH 4.5, 40% 1,2-propanediol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 7, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→40 Å / Num. obs: 21555 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 37.78 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.15→2.18 Å / Num. unique obs: 880 / CC1/2: 0.734 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→34.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
|