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- PDB-4ngv: Previously de-ionized HEW lysozyme batch crystallized in 0.5 M YbCl3 -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ngv | ||||||
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Title | Previously de-ionized HEW lysozyme batch crystallized in 0.5 M YbCl3 | ||||||
![]() | Lysozyme C | ||||||
![]() | HYDROLASE / Hofmeister series / protein cation interactions / ESI-mass spectrometry | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Benas, P. / Legrand, L. / Ries-Kautt, M. | ||||||
![]() | ![]() Title: Weak protein-cationic co-ion interactions addressed by X-ray crystallography and mass spectrometry. Authors: Benas, P. / Auzeil, N. / Legrand, L. / Brachet, F. / Regazzetti, A. / Ries-Kautt, M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2002 Title: Strong and specific effects of cations on lysozyme chloride solubility. Authors: Benas, P. / Legrand, L. / Ries-Kautt, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.5 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 415.7 KB | Display | ![]() |
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Full document | ![]() | 415.7 KB | Display | |
Data in XML | ![]() | 7.8 KB | Display | |
Data in CIF | ![]() | 10 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4nebC ![]() 4nfvC ![]() 4ng1C ![]() 4ng8C ![]() 4ngiC ![]() 4ngjC ![]() 4ngkC ![]() 4nglC ![]() 4ngoC ![]() 4ngwC ![]() 4ngyC ![]() 4ngzC ![]() 193lS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: HEW LYSOZYME / Source method: isolated from a natural source / Source: (natural) ![]() ![]() | ||||
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#2: Chemical | #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.05 Å3/Da / Density % sol: 39.92 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: Previously de-ionized lysozyme, no buffer added, 0.5 M YbCl3, pH 4.5, Batch crystallization, temperature 293K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 6, 2000 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9464 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→27.26 Å / Num. obs: 15095 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 16.9 Å2 / Rsym value: 0.067 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.64→1.7 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.298 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 193L Resolution: 1.64→55.79 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.959 / SU B: 3.546 / SU ML: 0.061 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.731 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.64→55.79 Å
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Refine LS restraints |
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