+
Open data
-
Basic information
Entry | Database: PDB / ID: 1p7s | ||||||
---|---|---|---|---|---|---|---|
Title | T4 LYSOZYME CORE REPACKING MUTANT V103I/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 | ![]() | 50.1 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 34.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 421.8 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 422.8 KB | Display | |
Data in XML | ![]() | 10.3 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p2lC ![]() 1p2rC ![]() 1p36C ![]() 1p37C ![]() 1p3nC ![]() 1p46C ![]() 1p64C ![]() 1p6yC ![]() 1pqdC ![]() 1pqiC ![]() 1pqjC ![]() 1pqkC ![]() 1pqmC ![]() 1pqoC ![]() 1l63S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 18642.389 Da / Num. of mol.: 1 / Mutation: C54T/C97A/V103I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.53 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: 2M K/Na phosphate, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 2002 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23979 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→22.086 Å / Num. all: 23577 / Num. obs: 23577 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.163 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2748 / Rsym value: 0.351 / % possible all: 77.9 |
Reflection | *PLUS Highest resolution: 1.5 Å |
Reflection shell | *PLUS % possible obs: 78 % |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: pdb entry 1L63 Resolution: 1.5→22.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT Details: THE WORKING SET AND TEST SET WERE NOT COMBINED DURING THE LAST STAGE OF REFINEMENT. THE OVERALL ANISOTROPIC B-VALUES ARE B11=0.34, B22=-0.02, B12=B13=B23=0.0, B33=-1.32
| |||||||||||||||||||||||||
Solvent computation | Solvent model: TNT / Bsol: 248.48 Å2 / ksol: 0.85 e/Å3 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→22.6 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.1 |