[English] 日本語
![](img/lk-miru.gif)
- PDB-5k59: Crystal structure of LukGH from Staphylococcus aureus in complex ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5k59 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of LukGH from Staphylococcus aureus in complex with a neutralising antibody | ||||||
![]() |
| ||||||
![]() | IMMUNE SYSTEM / toxin neutralizing monoclonal antibody / conformational epitope / X-ray crystal structure | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Welin, M. / Logan, D.T. / Badarau, A. / Mirkina, I. / Zauner, G. / Dolezilkova, I. / Nagy, E. | ||||||
![]() | ![]() Title: Context matters: The importance of dimerization-induced conformation of the LukGH leukocidin of Staphylococcus aureus for the generation of neutralizing antibodies. Authors: Badarau, A. / Rouha, H. / Malafa, S. / Battles, M.B. / Walker, L. / Nielson, N. / Dolezilkova, I. / Teubenbacher, A. / Banerjee, S. / Maierhofer, B. / Weber, S. / Stulik, L. / Logan, D.T. / ...Authors: Badarau, A. / Rouha, H. / Malafa, S. / Battles, M.B. / Walker, L. / Nielson, N. / Dolezilkova, I. / Teubenbacher, A. / Banerjee, S. / Maierhofer, B. / Weber, S. / Stulik, L. / Logan, D.T. / Welin, M. / Mirkina, I. / Pleban, C. / Zauner, G. / Gross, K. / Jagerhofer, M. / Magyarics, Z. / Nagy, E. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 790.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 680 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 377.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 407.7 KB | Display | |
Data in XML | ![]() | 68.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
|
-
Components
-Uncharacterized leukocidin-like protein ... , 2 types, 4 molecules DCBA
#1: Protein | Mass: 37143.102 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USA300 / Gene: SAUSA300_1975 / Production host: ![]() ![]() #2: Protein | Mass: 35825.539 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: USA300 / Gene: SAUSA300_1974 / Production host: ![]() ![]() |
---|
-Antibody , 2 types, 4 molecules HELF
#3: Antibody | Mass: 24166.100 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Antibody | Mass: 23338.846 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Non-polymers , 4 types, 7 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CL / |
---|---|
#6: Chemical | ChemComp-PO4 / |
#7: Chemical | ChemComp-PG4 / |
#8: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.4 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.2 Details: Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed ...Details: Drop contained 200 nl Fab-LukGH at 1:1 ratio + 50 nl seed stock + 150 nl reservoir solution [0.3 M NaCl, 26% polyethylene glycol (PEG) 8000, 0.1 M phosphate citrate pH 4.2]. The seed solution was obtained from 40 % PEG 300, 0.1 M phosphate-citrate pH 4.2, 0.3 M NaCl, 20 mM HEPES pH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 1, 2014 / Details: focusing mirrors |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→48.8 Å / Num. obs: 64655 / % possible obs: 99.3 % / Redundancy: 3.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.108 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 2.84→2.91 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.4 / % possible all: 92.5 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 73.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.84→48.54 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|