[English] 日本語
![](img/lk-miru.gif)
- PDB-6d2p: Crystal structure of IOMA-class CLK31 Fab from an HIV-1 naive don... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6d2p | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of IOMA-class CLK31 Fab from an HIV-1 naive donor in complex with a germline-targeting gp120 engineered outer domain eOD-GT8 at 2.6 A | ||||||
![]() |
| ||||||
![]() | ![]() | ||||||
Function / homology | ![]() ![]() ![]() ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sarkar, A. / Wilson, I.A. | ||||||
![]() | ![]() Title: The human naive B cell repertoire contains distinct subclasses for a germline-targeting HIV-1 vaccine immunogen. Authors: Havenar-Daughton, C. / Sarkar, A. / Kulp, D.W. / Toy, L. / Hu, X. / Deresa, I. / Kalyuzhniy, O. / Kaushik, K. / Upadhyay, A.A. / Menis, S. / Landais, E. / Cao, L. / Diedrich, J.K. / Kumar, S. ...Authors: Havenar-Daughton, C. / Sarkar, A. / Kulp, D.W. / Toy, L. / Hu, X. / Deresa, I. / Kalyuzhniy, O. / Kaushik, K. / Upadhyay, A.A. / Menis, S. / Landais, E. / Cao, L. / Diedrich, J.K. / Kumar, S. / Schiffner, T. / Reiss, S.M. / Seumois, G. / Yates, J.R. / Paulson, J.C. / Bosinger, S.E. / Wilson, I.A. / Schief, W.R. / Crotty, S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 129.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 97.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5iesS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 19889.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
---|---|---|---|
#2: Antibody | Mass: 23697.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#3: Antibody | Mass: 22417.773 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
#4: Chemical | ChemComp-GOL / ![]() #5: Water | ChemComp-HOH / | ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.48 % |
---|---|
Crystal grow![]() | Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: pH 5.0 of 20% w/v PEG6000, 0.1M citric acid (pH 4.0) |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.6→38.26 Å / Num. obs: 21985 / % possible obs: 99.9 % / Redundancy: 10.9 % / CC1/2: 0.92 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 10.8 % / Num. unique obs: 2165 / CC1/2: 0.31 / % possible all: 100 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure![]() ![]() Starting model: 5IES Resolution: 2.6→38.259 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 26.22 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.259 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|