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Yorodumi- PDB-1lys: X-RAY STRUCTURE OF A MONOCLINIC FORM OF HEN EGG-WHITE LYSOZYME CR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lys | ||||||
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Title | X-RAY STRUCTURE OF A MONOCLINIC FORM OF HEN EGG-WHITE LYSOZYME CRYSTALLIZED AT 313K. COMPARISON OF TWO INDEPENDENT MOLECULES | ||||||
Components | HEN EGG WHITE LYSOZYME | ||||||
Keywords | 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 / Resolution: 1.72 Å | ||||||
Authors | Harata, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: X-ray structure of a monoclinic form of hen egg-white lysozyme crystallized at 313 K. Comparison of two independent molecules. Authors: Harata, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lys.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lys.ent.gz | 48.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lys.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/1lys ftp://data.pdbj.org/pub/pdb/validation_reports/ly/1lys | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9998, -0.0425, 0.0241), Vector: |
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.79 Å3/Da / Density % sol: 31.11 % | ||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 313 K / pH: 7.6 / Method: unknown / Details: pH was adjusted to 7.6 with 0.1 M HCl | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.72 Å / Num. obs: 18391 / % possible obs: 87.5 % / Rmerge(I) obs: 0.061 |
-Processing
Software |
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Refinement | Resolution: 1.72→10 Å / Rfactor Rwork: 0.187 / Rfactor obs: 0.187 / σ(F): 3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.72 Å / Lowest resolution: 10 Å / Num. reflection obs: 18260 / σ(F): 3 / Rfactor obs: 0.187 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3 |