[English] 日本語
![](img/lk-miru.gif)
- PDB-4xcy: Crystal structure of human 4E10 Fab in complex with phosphatidylg... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4xcy | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human 4E10 Fab in complex with phosphatidylglycerol (06:0 PG) | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / 4E10 Fab anti HIV-1 gp41 MPER / membrane lipids / phosphatidylglycerol | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-44G / Unknown ligand![]() | ||||||
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 | ![]() | 436.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 359.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4xawC ![]() 4xbeC ![]() 4xbgC ![]() 4xbpC ![]() 4xc1C ![]() 4xc3C ![]() 4xccC ![]() 4xceC ![]() 4xcfC ![]() 4xcnC ![]() 2fx7S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
3 | ![]()
| ||||||||
4 | ![]()
| ||||||||
5 | ![]()
| ||||||||
6 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Antibody | Mass: 23395.850 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Antibody | Mass: 24180.250 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #3: Chemical | ChemComp-UNL / Num. of mol.: 5 / Source method: obtained synthetically #4: Chemical | #5: Chemical | ChemComp-GOL / | Nonpolymer details | FIVE UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTION ...FIVE UNKNOWN LIGANDS (UNL) HAVE BEEN MODELED. BASED ON ELECTRON DENSITY AND INTERACTIO | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.79 Å3/Da / Density % sol: 55.6 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6 Details: DROP CONTAINS 10 MG/ML 4E10 FAB, 10 MM PHOSPHATIDYLGLYCEROL (06:0 PG) MIXED 1:1 V/V WITH RESERVOIR SOLUTION OF 0.2 M SODIUM IODIDE, 20% PEG 3350, PH 6.0, VAPOR DIFFUSION, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2013 |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, non fixed exit slit Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.96→48.907 Å / Num. obs: 27268 / % possible obs: 95.5 % / Redundancy: 4.43 % / Biso Wilson estimate: 62.9 Å2 / Rsym value: 0.303 / Net I/σ(I): 5.2 |
Reflection shell | Resolution: 3.96→4.06 Å / Redundancy: 4.16 % / Rmerge(I) obs: 0.711 / Mean I/σ(I) obs: 2.1 / % possible all: 97.4 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2FX7 Resolution: 3.96→48.907 Å / SU ML: 1.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.77 Å2 / ksol: 0.31 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.8 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.96→48.907 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|