[English] 日本語
![](img/lk-miru.gif)
- PDB-4lxc: The antimicrobial peptidase lysostaphin from Staphylococcus simulans -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4lxc | ||||||
---|---|---|---|---|---|---|---|
Title | The antimicrobial peptidase lysostaphin from Staphylococcus simulans | ||||||
![]() | Lysostaphin | ||||||
![]() | HYDROLASE / PEPTIDASE FAMILY M23 / PEPTIDOGLYCAN HYDROLASE / METALLOPEPTIDASE / PEPTIDOGLYCAN | ||||||
Function / homology | ![]() lysostaphin / septum digestion after cytokinesis / cell division site / cell outer membrane / cell wall organization / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sabala, I. / Jagielska, E. / Bardelang, P.T. / Czapinska, H. / Dahms, S.O. / Sharpe, J.A. / James, R. / Than, M.E. / Thomas, N.R. / Bochtler, M. | ||||||
![]() | ![]() Title: Crystal structure of the antimicrobial peptidase lysostaphin from Staphylococcus simulans. Authors: Sabala, I. / Jagielska, E. / Bardelang, P.T. / Czapinska, H. / Dahms, S.O. / Sharpe, J.A. / James, R. / Than, M.E. / Thomas, N.R. / Bochtler, M. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 361 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 298.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 4qp5C ![]() 4qpbC ![]() 1r77S ![]() 2b0pS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
4 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
5 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Refine code: 4
NCS ensembles :
|
-
Components
#1: Protein | Mass: 28177.551 Da / Num. of mol.: 4 / Fragment: unp residues 248-493 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 8.29 Å3/Da / Density % sol: 85.17 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1 M MES and 1.6 M magnesium sulphate, 2 mM tetraglycine phosphinic acid. EDTA and ammonium sulphate as additives improved crystal quality, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2013 |
Radiation | Monochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→50 Å / Num. all: 48693 / Num. obs: 48693 / % possible obs: 100 % / Redundancy: 36.4 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.295 / Rsym value: 0.295 / Net I/σ(I): 17.34 |
Reflection shell | Resolution: 3.5→3.59 Å / Redundancy: 37.9 % / Rmerge(I) obs: 0.908 / Mean I/σ(I) obs: 5.34 / Num. unique all: 3539 / Rsym value: 0.908 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entries 1R77, 2B0P Resolution: 3.5→47.67 Å / Cor.coef. Fo:Fc: 0.823 / Cor.coef. Fo:Fc free: 0.796 / Cross valid method: THROUGHOUT / ESU R: 0.659 / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS AND TLS REFINEMENT HAS BEEN USED. DEPENDING ON THE RESOLUTION CUTOFF WE OBSERVED A WILSON B VALUE IN THE RANGE OF 30 AND 80 AND KEPT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. NCS AND TLS REFINEMENT HAS BEEN USED. DEPENDING ON THE RESOLUTION CUTOFF WE OBSERVED A WILSON B VALUE IN THE RANGE OF 30 AND 80 AND KEPT THE ATOMIC B AT A FIXED VALUE OF 36 OBSERVED FOR THE DEPOSITED DATA CUTOFF.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.566 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.5→47.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|