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- PDB-5vnq: Neutron crystallographic structure of perdeuterated T4 lysozyme c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5vnq | ||||||
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Title | Neutron crystallographic structure of perdeuterated T4 lysozyme cysteine-free pseudo-wild type at cryogenic temperature | ||||||
![]() | Endolysin | ||||||
![]() | HYDROLASE / T4 lysozyme / Neutron Crystallography / Hydrogen bonding network / Hydrogen bond / Water | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | NEUTRON DIFFRACTION / NUCLEAR REACTOR / ![]() | ||||||
![]() | Li, L. / Shukla, S. / Meilleur, F. / Standaert, R.F. / Pierce, J. / Myles, D.A.A. / Cuneo, M.J. | ||||||
![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.8 KB | Display | ![]() |
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PDB format | ![]() | 61.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 320.3 KB | Display | ![]() |
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Full document | ![]() | 320.4 KB | Display | |
Data in XML | ![]() | 5 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5vnrC ![]() 1lw9S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 18628.363 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | #3: Chemical | ChemComp-DOD / | |
-Experimental details
-Experiment
Experiment | Method: NEUTRON DIFFRACTION / Number of used crystals: 1 |
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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 |
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-Data collection
Diffraction | Mean temperature: 80 K | |||||||||
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Diffraction source | Source: NUCLEAR REACTOR / Site: ORNL High Flux Isotope Reactor ![]() | |||||||||
Detector | Type: FUJI / Detector: IMAGE PLATE / Date: Oct 4, 2016 | |||||||||
Radiation | Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron | |||||||||
Radiation wavelength |
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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 |
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Processing
Software | Name: PHENIX / Version: (1.11.1_2575: ???) / Classification: refinement | ||||||||||||||||||||||||
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Refinement | Method to determine structure: ![]() 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
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refine LS restraints |
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LS refinement shell | Resolution: 2.1829→16.6495 Å
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