+Open data
-Basic information
Entry | Database: PDB / ID: 7l3j | ||||||
---|---|---|---|---|---|---|---|
Title | T4 Lysozyme L99A - benzylacetate - RT | ||||||
Components | EndolysinLysin | ||||||
Keywords | HYDROLASE / RT / benzylacetate / L99A | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å | ||||||
Authors | Fischer, M. / Bradford, S.Y.C. | ||||||
Citation | Journal: Chem Sci / Year: 2021 Title: Temperature artifacts in protein structures bias ligand-binding predictions. Authors: Bradford, S.Y.C. / El Khoury, L. / Ge, Y. / Osato, M. / Mobley, D.L. / Fischer, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7l3j.cif.gz | 88.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7l3j.ent.gz | 65.4 KB | Display | PDB format |
PDBx/mmJSON format | 7l3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l3/7l3j ftp://data.pdbj.org/pub/pdb/validation_reports/l3/7l3j | HTTPS FTP |
---|
-Related structure data
Related structure data | 7l37C 7l38C 7l39C 7l3aC 7l3bC 7l3cC 7l3dC 7l3eC 7l3fC 7l3gC 7l3hC 7l3iC 7l3kC 4w51S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18620.387 Da / Num. of mol.: 1 / Mutation: R12G/I137R/L99A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme |
---|
-Non-polymers , 5 types, 92 molecules
#2: Chemical | ChemComp-TRS / |
---|---|
#3: Chemical | ChemComp-BME / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-J0Z / |
#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: 2.84 Å3/Da / Density % sol: 56.63 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Crystals were grown from a 10 mg/mL frozen protein solution by the hanging drop method at 291-293K, with a 1:1 drop ratio of protein to solution and over a well solution of 0.1 M Tris- ...Details: Crystals were grown from a 10 mg/mL frozen protein solution by the hanging drop method at 291-293K, with a 1:1 drop ratio of protein to solution and over a well solution of 0.1 M Tris-hydrochloride (pH 8), 20%-26% (w/v) PEG 4000, 70-170 mM lithium citrate, 8%-18% 2-propanol, 50 mM 2-mercaptoethanol, and 50 mM 2-hydroxyethyl disulfide Temp details: 291-293 |
-Data collection
Diffraction | Mean temperature: 278 K / Ambient temp details: RT / Serial crystal experiment: N | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å | ||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||
Reflection | Resolution: 1.49→52.93 Å / Num. obs: 33556 / % possible obs: 95.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 11.9 | ||||||||||||||||||
Reflection shell |
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4w51 Resolution: 1.49→52.926 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.23 / Stereochemistry target values: ML
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 73.32 Å2 / Biso mean: 23.8306 Å2 / Biso min: 12.58 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.49→52.926 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|