+Open data
-Basic information
Entry | Database: PDB / ID: 4y68 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a lipoprotein from Streptococcus agalactiae | ||||||
Components | Putative nisin-resistance protein | ||||||
Keywords | HYDROLASE / lipoprotein / lantibiotic / peptidase | ||||||
Function / homology | tail specific protease / Tail specific protease / Peptidase family S41 / ClpP/crotonase-like domain superfamily / serine-type peptidase activity / Putative nisin-resistance protein / : Function and homology information | ||||||
Biological species | Streptococcus agalactiae 515 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å | ||||||
Authors | Khosa, S. / Hoeppner, A. / Smits, S.H. | ||||||
Citation | Journal: Sci Rep / Year: 2016 Title: Structural basis of lantibiotic recognition by the nisin resistance protein from Streptococcus agalactiae. Authors: Khosa, S. / Frieg, B. / Mulnaes, D. / Kleinschrodt, D. / Hoeppner, A. / Gohlke, H. / Smits, S.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4y68.cif.gz | 241.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4y68.ent.gz | 201.3 KB | Display | PDB format |
PDBx/mmJSON format | 4y68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y6/4y68 ftp://data.pdbj.org/pub/pdb/validation_reports/y6/4y68 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35456.445 Da / Num. of mol.: 4 / Fragment: UNP residues 28-320 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus agalactiae 515 (bacteria) Gene: SAL_1042 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q3DLX7, UniProt: A0A140UHB6*PLUS #2: Chemical | ChemComp-MES / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.28 % |
---|---|
Crystal grow | Temperature: 297 K / Method: vapor diffusion / Details: 0.5 M lithium sulfate and 15% (w/v) PEG 8000 / PH range: 6-6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→100 Å / Num. obs: 67177 / % possible obs: 99.6 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.67 |
Reflection shell | Resolution: 2.21→2.29 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 1.8 / Num. unique all: 6695 / % possible all: 99.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.21→55.358 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.71 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→55.358 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|