+Open data
-Basic information
Entry | Database: PDB / ID: 1dpx | ||||||
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Title | STRUCTURE OF HEN EGG-WHITE LYSOZYME | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE / PROTEIN-CHLORIDE COMPLEX | ||||||
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 / Resolution: 1.65 Å | ||||||
Authors | Weiss, M.S. / Palm, G.J. / Hilgenfeld, R. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization, structure solution and refinement of hen egg-white lysozyme at pH 8.0 in the presence of MPD. Authors: Weiss, M.S. / Palm, G.J. / Hilgenfeld, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dpx.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dpx.ent.gz | 28.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dp/1dpx ftp://data.pdbj.org/pub/pdb/validation_reports/dp/1dpx | HTTPS FTP |
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-Related 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) / Tissue: EGG-WHITE / References: UniProt: P00698, lysozyme | ||
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#2: Chemical | #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: 1.93 Å3/Da / Density % sol: 36.15 % | ||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: SODIUM ACETATE, SODIUM CHLORIDE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→99 Å / Num. obs: 13962 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.66 % / Biso Wilson estimate: 17.2 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 51 |
Reflection shell | Resolution: 1.65→1.71 Å / Rmerge(I) obs: 0.143 / % possible all: 100 |
Reflection | *PLUS Num. measured all: 176694 |
Reflection shell | *PLUS % possible obs: 100 % / Mean I/σ(I) obs: 19.4 |
-Processing
Software |
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Refinement | Resolution: 1.65→40 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
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Refinement step | Cycle: LAST / Resolution: 1.65→40 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 40 Å / Num. reflection obs: 13267 / σ(F): 0 / Rfactor obs: 0.1874 / Rfactor Rfree: 0.2465 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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