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Open data
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Basic information
Entry | Database: PDB / ID: 1pqk | ||||||
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Title | Repacking of the Core of T4 Lysozyme by Automated Design | ||||||
![]() | 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 114.6 KB | Display | ![]() |
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PDB format | ![]() | 89.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.8 KB | Display | ![]() |
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Full document | ![]() | 466.2 KB | Display | |
Data in XML | ![]() | 24.7 KB | Display | |
Data in CIF | ![]() | 35.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1p2lC ![]() 1p2rC ![]() 1p36C ![]() 1p37C ![]() 1p3nC ![]() 1p46C ![]() 1p64C ![]() 1p6yC ![]() 1p7sC ![]() 1pqdC ![]() 1pqiC ![]() 1pqjC ![]() 1pqmC ![]() 1pqoC C: citing same article ( |
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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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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18706.410 Da / Num. of mol.: 3 Mutation: C54T, G77A, I78V, C97A, L118I, M120Y, L133F, V149I, T152V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % | |||||||||||||||||||||||||||||||||||
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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 pH: 6.7 / Method: vapor diffusion | |||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: May 23, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 2→23.702 Å / Num. obs: 40412 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.378 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.188 / % possible all: 95.2 |
Reflection | *PLUS Highest resolution: 2 Å |
Reflection shell | *PLUS % possible obs: 91 % |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Solvent model: TNT / Bsol: 292.675 Å2 / ksol: 0.93407 e/Å3 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→72.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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