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Yorodumi- PDB-4nfv: Previously de-ionized HEW lysozyme batch crystallized in 1.1 M MnCl2 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4nfv | ||||||
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Title | Previously de-ionized HEW lysozyme batch crystallized in 1.1 M MnCl2 | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / Hofmeister series / protein cation interactions / ESI-mass spectrometry | ||||||
Function / homology | Function and homology information Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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 | 4nfv.cif.gz | 70.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4nfv.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 4nfv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/4nfv ftp://data.pdbj.org/pub/pdb/validation_reports/nf/4nfv | HTTPS FTP |
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-Related structure data
Related structure data | 4nebC 4ng1C 4ng8C 4ngiC 4ngjC 4ngkC 4nglC 4ngoC 4ngvC 4ngwC 4ngyC 4ngzC 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 | ChemComp-CL / | #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: 2.09 Å3/Da / Density % sol: 41.28 % |
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Crystal grow | Temperature: 293 K / pH: 4.5 Details: Previously de-ionized lysozyme, no buffer added, 1.1 M MnCl2, pH 4.5, Batch crystallization, temperature 293K |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: D41A / Wavelength: 1.388 |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Nov 30, 2000 / Details: MIRRORS |
Radiation | Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.388 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→27.445 Å / Num. obs: 215410 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Biso Wilson estimate: 17.7 Å2 / Rsym value: 0.075 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.63→1.69 Å / Redundancy: 12.8 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.37 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 193L Resolution: 1.63→27.445 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.155 / SU ML: 0.053 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / 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: 22.729 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.63→27.445 Å
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Refine LS restraints |
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