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Open data
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Basic information
Entry | Database: PDB / ID: 1dkk | ||||||
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Title | BOBWHITE QUAIL LYSOZYME WITH NITRATE | ||||||
![]() | LYSOZYME | ||||||
![]() | HYDROLASE (O-GLYCOSYL) / HYDROLASE / GLYCOSIDASE / BACTERIOLYTIC ENZYME | ||||||
Function / homology | ![]() lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() | ||||||
![]() | Jeffrey, P.D. / Sheriff, S. | ||||||
![]() | ![]() Title: Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment. Authors: Chacko, S. / Silverton, E.W. / Smith-Gill, S.J. / Davies, D.R. / Shick, K.A. / Xavier, K.A. / Willson, R.C. / Jeffrey, P.D. / Chang, C.Y. / Sieker, L.C. / Sheriff, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.1 KB | Display | ![]() |
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PDB format | ![]() | 47.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.97169, 0.225451, -0.070642), Vector: |
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Components
#1: Protein | Mass: 14289.119 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 34 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: May 1, 1989 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 14910 / % possible obs: 85 % / Redundancy: 3 % / Rmerge(I) obs: 0.037 |
Reflection | *PLUS Highest resolution: 1.9 Å / % possible obs: 85 % / Num. measured all: 43399 / Rmerge(I) obs: 0.0367 |
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Processing
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Refinement | Resolution: 1.9→6 Å / σ(F): 1 /
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Refinement step | Cycle: LAST / Resolution: 1.9→6 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.157 | ||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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