[English] 日本語
![](img/lk-miru.gif)
- PDB-4xbp: Crystal structure of human 4E10 Fab crystalized in the presence o... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4xbp | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human 4E10 Fab crystalized in the presence of Phosphatidylethanolamine (06:0 PE) | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / human 4E10 Fab anti HIV-1 gp41 / membrane lipids / Phosphatidylethanolamine | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Irimia, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Crystallographic Identification of Lipid as an Integral Component of the Epitope of HIV Broadly Neutralizing Antibody 4E10. Authors: Irimia, A. / Sarkar, A. / Stanfield, R.L. / Wilson, I.A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 328.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 263.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 494.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 507.3 KB | Display | |
Data in XML | ![]() | 57.6 KB | Display | |
Data in CIF | ![]() | 78.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4xawC ![]() 4xbeC ![]() 4xbgC ![]() 4xc1C ![]() 4xc3C ![]() 4xccC ![]() 4xceC ![]() 4xcfC ![]() 4xcnC ![]() 4xcyC ![]() 2fx7S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24180.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 47.9 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 Details: Sitting drops contain 4E10 Fab at 10 mg/ml, 10 mM Phosphatidylethanolamine (06:0 PE) sample stock mixed (1:1 ratio) with reservoir solution of 20% PEG 6000, 0.1M Tris, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 17, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03323 Å / Relative weight: 1 |
Reflection | Resolution: 2.94→49.159 Å / Num. obs: 33714 / % possible obs: 92.7 % / Redundancy: 4 % / Biso Wilson estimate: 22.8 Å2 / Rsym value: 0.178 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.94→3 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 1.9 / % possible all: 94.5 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 2FX7 Resolution: 2.94→49.159 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.81 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.1 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.94→49.159 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|