+
Open data
-
Basic information
Entry | Database: PDB / ID: 1pqo | ||||||
---|---|---|---|---|---|---|---|
Title | T4 Lysozyme Core Repacking Mutant L118I/TA | ||||||
![]() | Lysozyme | ||||||
![]() | 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 | ![]() 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 | ![]() ![]() | ||||||
![]() | Mooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W. | ||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 50.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 426.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 429.6 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p2lC ![]() 1p2rC ![]() 1p36C ![]() 1p37C ![]() 1p3nC ![]() 1p46C ![]() 1p64C ![]() 1p6yC ![]() 1p7sC ![]() 1pqdC ![]() 1pqiC ![]() 1pqjC ![]() 1pqkC ![]() 1pqmC ![]() 1l63S C: citing same article ( 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 / Mutation: C54T/C97A/L118I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-K / | ||||
#3: Chemical | #4: Chemical | ChemComp-HED / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.27 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / pH: 6.7 Details: Potassium phosphate, sodium PHOSPHATE, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.70 | ||||||||||||||||||||||||||||||
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: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 10, 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 | Resolution: 1.65→18.7 Å / Num. obs: 23077 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 24.296 Å2 / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.65→1.72 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.3 / % possible all: 91.2 |
Reflection | *PLUS Highest resolution: 1.65 Å |
Reflection shell | *PLUS % possible obs: 91 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L63 Resolution: 1.65→18.7 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT
| ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→18.7 Å
| ||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.201 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.3 |