+Open data
-Basic information
Entry | Database: PDB / ID: 2cds | ||||||
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Title | LYSOZYME | ||||||
Components | PROTEIN (LYSOZYME (E.C.3.2.1.17)) | ||||||
Keywords | HYDROLASE / HYDROLASE (O-GLYCOSYL) | ||||||
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 / OTHER / Resolution: 2 Å | ||||||
Authors | Kleywegt, G.J. / Divne, C. | ||||||
Citation | Journal: To be Published Title: Structure of Lysozyme Authors: Kleywegt, G.J. / Divne, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2cds.cif.gz | 37.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cds.ent.gz | 25.5 KB | Display | PDB format |
PDBx/mmJSON format | 2cds.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cd/2cds ftp://data.pdbj.org/pub/pdb/validation_reports/cd/2cds | HTTPS FTP |
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-Related structure data
Related structure data | 8lyzS 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: 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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.52 % |
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Crystal grow | pH: 7 / Details: pH 7 |
-Data collection
Diffraction | Mean temperature: 285 K |
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Diffraction source | Wavelength: 1.5418 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→40 Å / Num. obs: 8398 / % possible obs: 98.4 % / Redundancy: 12.8 % / Rsym value: 0.066 / Net I/σ(I): 8.9 |
-Processing
Software | Name: CNS / Version: 0.4 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: OTHER Starting model: 8LYZ Resolution: 2→40 Å / Cross valid method: THROUGHOUT EXCEPT FINAL ROUND / σ(F): 0 Details: The author has informed us that water molecule hoh 228 could well be a small cation instead (probably sodium)
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Solvent computation | Bsol: 62 Å2 / ksol: 0.37 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→40 Å
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Refine LS restraints |
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