[English] 日本語
Yorodumi- PDB-8p8e: Crystal structure of endolysin gp46 from Pseudomonas aeruginosa b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8p8e | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of endolysin gp46 from Pseudomonas aeruginosa bacteriophage vB_PaeM_KTN6 | |||||||||
Components | Glycoside hydrolase family protein | |||||||||
Keywords | HYDROLASE / endolysin / phage lysozyme / muramidase / antimicrobial | |||||||||
Function / homology | Glycoside hydrolase, family 19, catalytic / Chitinase class I / chitinase activity / chitin catabolic process / cell wall macromolecule catabolic process / Lysozyme-like domain superfamily / DI(HYDROXYETHYL)ETHER / Glycoside hydrolase family protein Function and homology information | |||||||||
Biological species | Bacteriophage sp. (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.391 Å | |||||||||
Authors | van Raaij, M.J. / Sanz-Gaitero, M. | |||||||||
Funding support | Spain, 2items
| |||||||||
Citation | Journal: PHAGE / Year: 2024 Title: Structural and Biochemical Characterization of a New Phage-Encoded Muramidase, KTN6 Gp46 Authors: Sanz-Gaitero, M. / De Maesschalck, V. / Patel, A. / Longin, H. / Van Noort, V. / Rodriguez-Rubio, L. / van Ryne, M. / Danis-Wlodarczyk, K. / Drulis-Kawa, Z. / Mesnage, S. / van Raaij, M. / Lavigne, R. #1: Journal: PLoS One / Year: 2015 Title: Characterization of the Newly Isolated Lytic Bacteriophages KTN6 and KT28 and Their Efficacy against Pseudomonas aeruginosa Biofilm. Authors: Danis-Wlodarczyk, K. / Olszak, T. / Arabski, M. / Wasik, S. / Majkowska-Skrobek, G. / Augustyniak, D. / Gula, G. / Briers, Y. / Jang, H.B. / Vandenheuvel, D. / Duda, K.A. / Lavigne, R. / Drulis-Kawa, Z. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8p8e.cif.gz | 105 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8p8e.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 8p8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p8/8p8e ftp://data.pdbj.org/pub/pdb/validation_reports/p8/8p8e | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 24199.422 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacteriophage sp. (virus) / Gene: IDBGMNHM_00003 / Plasmid: pEXP5-CT/TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): Lemo21 / Variant (production host): DE3 / References: UniProt: A0A9E7MJ36 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-PEG / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.05 % / Description: needle |
---|---|
Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop Details: 10 mM HEPES-NaOH pH 7.0; 10 mM trisodium citrate; 16% (w/v) PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97929 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 1.39→43.2 Å / Num. obs: 46757 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 17.995 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.026 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.39→1.47 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.002 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6679 / CC1/2: 0.695 / Rpim(I) all: 0.425 / % possible all: 99.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.391→40.003 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 2.033 / SU ML: 0.035 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.049 Details: Hydrogens have been added in their riding positions
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.118 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.391→40.003 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
|