+Open data
-Basic information
Entry | Database: PDB / ID: 1pqj | ||||||
---|---|---|---|---|---|---|---|
Title | T4 LYSOZYME CORE REPACKING MUTANT A111V/CORE10/TA | ||||||
Components | Lysozyme | ||||||
Keywords | HYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / DESIGNED CORE MUTANT / AUTOMATED PROTEIN DESIGN / PROTEIN ENGINEERING / PROTEIN FOLDING / PROTEIN STABILITY / CORE REPACKING / BACK REVERTANT / DEAD-END ELIMINATION THEOREM / SIDE-CHAIN PACKING / OPTIMIZED ROTAMER COMBINATIONS / ORBIT | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Mooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: REPACKING THE CORE OF T4 LYSOZYME BY AUTOMATED DESIGN Authors: Mooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pqj.cif.gz | 50.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pqj.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pqj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/1pqj ftp://data.pdbj.org/pub/pdb/validation_reports/pq/1pqj | HTTPS FTP |
---|
-Related structure data
Related structure data | 1p2lC 1p2rC 1p36C 1p37C 1p3nC 1p46C 1p64C 1p6yC 1p7sC 1pqdC 1pqiC 1pqkC 1pqmC 1pqoC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18684.361 Da / Num. of mol.: 1 Mutation: C54T/V87I/C97A/I100V/M102L/V103I/M106I/V111A/M120Y/L133F/V149I/T152V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-K / | ||||
#3: Chemical | #4: Chemical | ChemComp-HED / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.94 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: Potassium phosphate, Sodium PHOSPHATE, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / Details: Eriksson, A.E., (1993) J.Mol.Biol., 229, 747. / PH range low: 7.1 / PH range high: 6.3 | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 27, 2001 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 22 Å2 |
Reflection | *PLUS Highest resolution: 1.9 Å / % possible obs: 99 % / Rmerge(I) obs: 0.061 |
Reflection shell | *PLUS % possible obs: 100 % |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY lL63 Resolution: 1.9→21.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: tnt
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement step | Cycle: LAST / Resolution: 1.9→21.7 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Rfactor Rwork: 0.188 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
|