[English] 日本語
Yorodumi- PDB-6srt: Endolysine N-acetylmuramoyl-L-alanine amidase LysCS from Clostrid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6srt | ||||||
---|---|---|---|---|---|---|---|
Title | Endolysine N-acetylmuramoyl-L-alanine amidase LysCS from Clostridium intestinale URNW | ||||||
Components | N-acetylmuramoyl-L-alanine amidase | ||||||
Keywords | HYDROLASE / endolysine / zinc binding / amidase / cell wall degradation | ||||||
Function / homology | Function and homology information N-acetylmuramoyl-L-alanine amidase activity / peptidoglycan catabolic process / zinc ion binding Similarity search - Function | ||||||
Biological species | Clostridium intestinale URNW (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å | ||||||
Authors | Hakansson, M. / Al-Karadaghi, S. / Plotka, M. / Kaczorowska, A.-K. / Kaczorowski, T. | ||||||
Funding support | Sweden, 1items
| ||||||
Citation | Journal: To Be Published Title: Structure and function of endolysines LysCS, LysC from Clostridium intestinale Authors: Plotka, M. / Hakansson, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6srt.cif.gz | 91.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6srt.ent.gz | 68.3 KB | Display | PDB format |
PDBx/mmJSON format | 6srt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sr/6srt ftp://data.pdbj.org/pub/pdb/validation_reports/sr/6srt | HTTPS FTP |
---|
-Related structure data
Related structure data | 6su5S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19401.857 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium intestinale URNW (bacteria) Gene: CINTURNW_1763 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: U2NM08 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.22 Å3/Da / Density % sol: 44.48 % |
---|---|
Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7.4 / Details: NaKHPO4, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97951 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 19, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97951 Å / Relative weight: 1 |
Reflection | Resolution: 1.21→44.2 Å / Num. obs: 48199 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 1 / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 1.21→1.23 Å / Rmerge(I) obs: 1.22 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2370 / CC1/2: 0.5 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6SU5 Resolution: 1.21→44.2 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.977 / SU B: 1.184 / SU ML: 0.023 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.036 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 93.18 Å2 / Biso mean: 16.913 Å2 / Biso min: 8.55 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.21→44.2 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.21→1.241 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|