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Yorodumi- PDB-4ngz: Previously de-ionized HEW lysozyme crystallized in 0.5 M YbCl3/30... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ngz | ||||||
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Title | Previously de-ionized HEW lysozyme crystallized in 0.5 M YbCl3/30% (v/v) glycerol and collected at 125K | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Hofmeister series / protein cation interactions / HEW lysozyme / ESI-mass spectrometry | ||||||
Function / homology | Function and homology information 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 | Gallus gallus (chicken) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Benas, P. / Legrand, L. / Ries-Kautt, M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ngz.cif.gz | 69.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ngz.ent.gz | 50.4 KB | Display | PDB format |
PDBx/mmJSON format | 4ngz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ngz_validation.pdf.gz | 423 KB | Display | wwPDB validaton report |
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Full document | 4ngz_full_validation.pdf.gz | 423.2 KB | Display | |
Data in XML | 4ngz_validation.xml.gz | 8.6 KB | Display | |
Data in CIF | 4ngz_validation.cif.gz | 11.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/4ngz ftp://data.pdbj.org/pub/pdb/validation_reports/ng/4ngz | HTTPS FTP |
-Related structure data
Related structure data | 4nebC 4nfvC 4ng1C 4ng8C 4ngiC 4ngjC 4ngkC 4nglC 4ngoC 4ngvC 4ngwC 4ngyC 193lS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme | ||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.32 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: Previously de-ionized lysozyme, no buffer added, 0.5 M YbCl3, 30% (v/v) glycerol , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 125 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: May 17, 2000 |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→19.65 Å / Num. obs: 13242 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 20.1 Å2 / Rsym value: 0.067 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.202 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.7→55.57 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.669 / SU ML: 0.067 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.113 / 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: 1.5 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.581 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→55.57 Å
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Refine LS restraints |
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