[English] 日本語
![](img/lk-miru.gif)
- PDB-6u3y: Structure-based discovery of a novel small-molecule inhibitor of ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6u3y | ||||||
---|---|---|---|---|---|---|---|
Title | Structure-based discovery of a novel small-molecule inhibitor of methicillin-resistant S. aureus | ||||||
![]() |
| ||||||
![]() | TOXIN / alpha-toxin / PVL / Leukocidins / MRSA | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Liu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structure-based discovery of a small-molecule inhibitor of methicillin-resistantStaphylococcus aureusvirulence. Authors: Liu, J. / Kozhaya, L. / Torres, V.J. / Unutmaz, D. / Lu, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 350 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 285.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 6u2sC ![]() 6u33C ![]() 6u3fC ![]() 6u3tC ![]() 6u49C ![]() 6u4pC ![]() 3b07S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 2 types, 3 molecules ABD
#1: Protein | Mass: 34494.039 Da / Num. of mol.: 1 / Fragment: UNP residues 25-325 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: lukF-PV, hlgB_1, lukF- PV, LukPV-F, lukPV-F, lukPVF, NCTC6133_01921 Production host: ![]() ![]() |
---|---|
#2: Protein | Mass: 32374.668 Da / Num. of mol.: 2 / Fragment: UNP residues 29-312 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: lukS-PV, LukPV-S, lukPV-S, lukPVS, EP54_02590, EQ90_09955 Production host: ![]() ![]() |
-Non-polymers , 4 types, 376 molecules ![](data/chem/img/PQJ.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-ACT / #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.22 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 6.7 mg/mL LukF-PV, 6.3 mg/mL LukS-PV, 10 mM sodium acetate, pH 5.4, 15 mM Fos-Choline-14, 40 mM beta-OG against reservoir solution of 0.16 M magnesium formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 17, 2018 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→38.7 Å / Num. obs: 76882 / % possible obs: 99.9 % / Redundancy: 12.8 % / CC1/2: 0.956 / Rmerge(I) obs: 0.098 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2.04→2.09 Å / Rmerge(I) obs: 0.981 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3741 / CC1/2: 0.754 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB entry 3B07 Resolution: 2.04→38.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.954 / SU ML: 0.105 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.146 / Details: U VALUES : WITH TLS ADDED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.19 Å2 / Biso mean: 44.123 Å2 / Biso min: 21.94 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→38.69 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.04→2.092 Å / Rfactor Rfree error: 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|