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Open data
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Basic information
Entry | Database: PDB / ID: 6d6e | ||||||
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Title | Triclinic lysozyme (295 K) in the presence of 47% xylose | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Glycosidase | ||||||
Function / homology | ![]() Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Juers, D.H. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The impact of cryosolution thermal contraction on proteins and protein crystals: volumes, conformation and order. Authors: Juers, D.H. / Farley, C.A. / Saxby, C.P. / Cotter, R.A. / Cahn, J.K.B. / Holton-Burke, R.C. / Harrison, K. / Wu, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 57.1 KB | Display | ![]() |
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PDB format | ![]() | 45.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5un3C ![]() 5uu7C ![]() 5uu8C ![]() 5uu9C ![]() 5uuaC ![]() 5uubC ![]() 5uucC ![]() 5uudC ![]() 5uueC ![]() 6avlC ![]() 6b6nC ![]() 6b6oC ![]() 6b6pC ![]() 6b6qC ![]() 6b6rC ![]() 6b6sC ![]() 6b6tC ![]() 6d5nC ![]() 6d5oC ![]() 6d5pC ![]() 6d5qC ![]() 6d5rC ![]() 6d5sC ![]() 6d5tC ![]() 6d5uC ![]() 6d6fC ![]() 6d6gC ![]() 6d6hC ![]() 6dzfC 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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Unit cell |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||
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#2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.42 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / Details: Protein: 10 mg/mL Well: 0.3 M NaNO3 |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Jan 19, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→13.67 Å / Num. obs: 6847 / % possible obs: 98.9 % / Redundancy: 3 % / CC1/2: 0.997 / Rrim(I) all: 0.071 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 2→2.11 Å / Mean I/σ(I) obs: 5.2 / CC1/2: 0.942 / Rrim(I) all: 0.241 |
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Processing
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Refinement | Resolution: 2→13.359 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 17.59
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→13.359 Å
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Refine LS restraints |
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LS refinement shell |
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