[English] 日本語
Yorodumi- PDB-5vnq: Neutron crystallographic structure of perdeuterated T4 lysozyme c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vnq | ||||||
---|---|---|---|---|---|---|---|
Title | Neutron crystallographic structure of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / T4 lysozyme / Neutron Crystallography / Hydrogen bonding network / Hydrogen bond / Water | ||||||
Function / homology | Function and homology information viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Li, L. / Shukla, S. / Meilleur, F. / Standaert, R.F. / Pierce, J. / Myles, D.A.A. / Cuneo, M.J. | ||||||
Citation | Journal: Protein Sci. / Year: 2017 Title: Neutron crystallographic studies of T4 lysozyme at cryogenic temperature. Authors: Li, L. / Shukla, S. / Meilleur, F. / Standaert, R.F. / Pierce, J. / Myles, D.A.A. / Cuneo, M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5vnq.cif.gz | 80.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5vnq.ent.gz | 61.4 KB | Display | PDB format |
PDBx/mmJSON format | 5vnq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vn/5vnq ftp://data.pdbj.org/pub/pdb/validation_reports/vn/5vnq | HTTPS FTP |
---|
-Related structure data
Related structure data | 5vnrC 1lw9S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18628.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Production host: Escherichia coli (E. coli) / References: UniProt: D9IEF7, UniProt: P00720*PLUS, lysozyme | ||
---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-DOD / | |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: ~2.0 M Na/K phosphate, pH 6-7, 250 mM NaCl, 40mM 2-hydroxyethyl disulfide PH range: 6-7 |
---|
-Data collection
Diffraction | Mean temperature: 80 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: NUCLEAR REACTOR / Site: ORNL High Flux Isotope Reactor / Beamline: CG4D / Wavelength: 2.8 - 4.6 | |||||||||
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Oct 4, 2016 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 2.2→16.7 Å / Num. obs: 7965 / % possible obs: 72.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.162 / Net I/σ(I): 6.5 | |||||||||
Reflection shell | Resolution: 2.2→2.32 Å / Rmerge(I) obs: 0.214 |
-Processing
Software | Name: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1LW9 Resolution: 2.2→16.7 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 18.63
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1829→16.6495 Å
|