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- PDB-3sb7: Cu-mediated Trimer of T4 Lysozyme D61H/K65H/R76H/R80H by Syntheti... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3sb7 | ||||||
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Title | Cu-mediated Trimer of T4 Lysozyme D61H/K65H/R76H/R80H by Synthetic Symmetrization | ||||||
![]() | Lysozyme | ||||||
![]() | HYDROLASE / metal-mediated synthetic symmetrization / synthetic symmetrization | ||||||
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 | ![]() ![]() ![]() ![]() | ||||||
![]() | Soriaga, A.B. / Laganowsky, A. / Zhao, M. / Sawaya, M.R. / Cascio, D. / Yeates, T.O. | ||||||
![]() | ![]() Title: An approach to crystallizing proteins by metal-mediated synthetic symmetrization. Authors: Laganowsky, A. / Zhao, M. / Soriaga, A.B. / Sawaya, M.R. / Cascio, D. / Yeates, T.O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.7 KB | Display | ![]() |
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PDB format | ![]() | 103.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.7 KB | Display | ![]() |
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Full document | ![]() | 445.3 KB | Display | |
Data in XML | ![]() | 13.6 KB | Display | |
Data in CIF | ![]() | 17.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3sb5C ![]() 3sb6C ![]() 3sb8C ![]() 3sb9C ![]() 3sbaC ![]() 3sbbC ![]() 3serC ![]() 3sesC ![]() 3setC ![]() 3seuC ![]() 3sevC ![]() 3sewC ![]() 3sexC ![]() 3seyC 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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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18606.254 Da / Num. of mol.: 2 / Mutation: C54T, D61H, K65H, R76H, R80H, C97A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-GOL / | #3: Chemical | ChemComp-CU / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.91 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 0.2M Potassium Thiocyanate, 25% PEG 3350, vapor diffusion, hanging drop, temperature 290K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 24, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→27.472 Å / Num. obs: 9419 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.633 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 9.75 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.178 Å2 / ksol: 0.343 e/Å3 | ||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.35 Å2 / Biso mean: 36.2864 Å2 / Biso min: 2.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→27.472 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3
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