[English] 日本語
Yorodumi- PDB-8f11: T4 lysozyme with a 2,6-diazaadamantane nitroxide (DZD) spin label -
+Open data
-Basic information
Entry | Database: PDB / ID: 8f11 | ||||||
---|---|---|---|---|---|---|---|
Title | T4 lysozyme with a 2,6-diazaadamantane nitroxide (DZD) spin label | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / spin label / glycan hydrolase | ||||||
Function / homology | Function and homology information cytolysis / 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 | Escherichia phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å | ||||||
Authors | Wilson, M.A. / Madzelan, P. / Rajca, A. / Stein, R. / Yang, Z. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Cucurbit[7]uril Enhances Distance Measurements of Spin-Labeled Proteins. Authors: Yang, Z. / Stein, R.A. / Pink, M. / Madzelan, P. / Ngendahimana, T. / Rajca, S. / Wilson, M.A. / Eaton, S.S. / Eaton, G.R. / Mchaourab, H.S. / Rajca, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8f11.cif.gz | 162.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8f11.ent.gz | 107.4 KB | Display | PDB format |
PDBx/mmJSON format | 8f11.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f1/8f11 ftp://data.pdbj.org/pub/pdb/validation_reports/f1/8f11 | HTTPS FTP |
---|
-Related structure data
Related structure data | 7lxaS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18602.326 Da / Num. of mol.: 1 / Mutation: C54T,C97A,K65C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia phage T4 (virus) / Production host: Escherichia coli (E. coli) / Strain (production host): K38 / References: UniProt: A0A7S9SVX7, lysozyme |
---|
-Non-polymers , 5 types, 307 molecules
#2: Chemical | #3: Chemical | ChemComp-X8R / | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.02 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: 1.6 M sodium/potassium phosphate pH 7.4, 100 mM NaCl, 40 mM beta mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.729 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 28, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.729 Å / Relative weight: 1 |
Reflection | Resolution: 1.12→35.2 Å / Num. obs: 77616 / % possible obs: 99.6 % / Redundancy: 13.7 % / Biso Wilson estimate: 14.04 Å2 / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.12→1.14 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3537 / CC1/2: 0.246 / Rrim(I) all: 3.729 / % possible all: 92.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7LXA Resolution: 1.12→35.2 Å / SU ML: 0.1055 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.9842 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.97 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.12→35.2 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|