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Open data
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Basic information
Entry | Database: PDB / ID: 1p2l | ||||||
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Title | T4 Lysozyme Core Repacking Mutant V87I/TA | ||||||
![]() | LYSOZYME | ||||||
![]() | HYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / DESIGNED CORE MUTANT / AUTOMATED PROTEIN DESIGN / PROTEIN ENGINEERING / PROTEIN FOLDING / PROTEIN STABILITY / CORE REPACKING / 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 54.5 KB | Display | ![]() |
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PDB format | ![]() | 37 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.5 KB | Display | ![]() |
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Full document | ![]() | 455 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p2rC ![]() 1p36C ![]() 1p37C ![]() 1p3nC ![]() 1p46C ![]() 1p64C ![]() 1p6yC ![]() 1p7sC ![]() 1pqdC ![]() 1pqiC ![]() 1pqjC ![]() 1pqkC ![]() 1pqmC ![]() 1pqoC ![]() 1l63S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 18642.389 Da / Num. of mol.: 1 / Mutation: C54T, V87I, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 244 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HED.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/K.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HED.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-PO4 / | ||||
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#3: Chemical | ChemComp-K / | ||||
#4: Chemical | #5: Chemical | ChemComp-HED / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: Potassium PHOSPHATE, Sodium Phosphate, NaCl, BME, 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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Aug 27, 2001 |
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: 1.58→22.7 Å / Num. all: 25789 / Num. obs: 25789 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.36 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.055 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 1.58→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3339 / Rsym value: 0.2 / % possible all: 77.4 |
Reflection shell | *PLUS % possible obs: 77 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1L63 Resolution: 1.58→22.7 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: TNT Details: Working and test sets were not combined in the last cycle of refinement.
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Solvent computation | Solvent model: TNT / Bsol: 173.29 Å2 / ksol: 0.78204 e/Å3 | |||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.58→22.7 Å
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Refine LS restraints |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 2.3 |