+Open data
-Basic information
Entry | Database: PDB / ID: 2zil | ||||||
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Title | Crystal Structure of Human Lysozyme from Urine | ||||||
Components | Lysozyme C | ||||||
Keywords | HYDROLASE / secreted protein from urine / Amyloid / Antimicrobial / Bacteriolytic enzyme / Disease mutation / Glycosidase / Polymorphism | ||||||
Function / homology | Function and homology information antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium ...antimicrobial humoral response / Antimicrobial peptides / metabolic process / specific granule lumen / azurophil granule lumen / tertiary granule lumen / 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 / inflammatory response / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Tamada, T. / Kuroki, R. / Koshiba, T. | ||||||
Citation | Journal: To be Published Title: Preparation and characterization of methyonyl-lysine attached human lysozyme expressed in Escherichia coli and its effective conversion to the authentic-like protein Authors: Shoyama, Y. / Tamada, T. / Nitta, K. / Kumagai, I. / Kuroki, R. / Koshiba, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zil.cif.gz | 41.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zil.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zil ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zil | HTTPS FTP |
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-Related structure data
Related structure data | 2zijC 2zikC 1i1zS 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
#1: Protein | Mass: 14720.693 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Urine / Source: (natural) Homo sapiens (human) / References: UniProt: P61626, lysozyme |
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#2: Chemical | ChemComp-NA / |
#3: 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 Å3/Da / Density % sol: 38.41 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 2.5M sodium chloride, 0.03M phosphate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 23, 2002 / Details: double-mirror |
Radiation | Monochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.52 Å / Num. all: 29167 / Num. obs: 11190 / % possible obs: 91.2 % / Rmerge(I) obs: 0.084 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I1Z Resolution: 1.8→41.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.899 / SU B: 3.179 / SU ML: 0.096 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.152 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.497 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→41.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.847 Å / Total num. of bins used: 20
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