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Yorodumi- PDB-4lym: CRYSTAL STRUCTURE OF LOW HUMIDITY TETRAGONAL LYSOZYME AT 2.1-ANGS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lym | ||||||
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Title | CRYSTAL STRUCTURE OF LOW HUMIDITY TETRAGONAL LYSOZYME AT 2.1-ANGSTROMS RESOLUTION. VARIABILITY IN HYDRATION SHELL AND ITS STRUCTURAL CONSEQUENCES | ||||||
Components | HEN EGG WHITE LYSOZYME | ||||||
Keywords | HYDROLASE (O-GLYCOSYL) | ||||||
Function / homology | Function and homology information Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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: 2.1 Å | ||||||
Authors | Kodandapani, R. / Suresh, C.G. / Vijayan, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 1990 Title: Crystal structure of low humidity tetragonal lysozyme at 2.1-A resolution. Variability in hydration shell and its structural consequences. Authors: Kodandapani, R. / Suresh, C.G. / Vijayan, M. #1: Journal: Curr.Sci. / Year: 1991 Title: Rigid and Flexible Regions in Lysozyme and the Invariant Features in its Hydration Shell Authors: Madhusudhan / Vijayan, M. #2: Journal: Acta Crystallogr.,Sect.B / Year: 1985 Title: Water-Mediated Transformations in Protein Crystals Authors: Salunke, D.M. / Veerapandian, B. / Kodandapani, R. / Vijayan, M. #3: Journal: Curr.Sci. / Year: 1984 Title: Water-Mediated Structural Transformations in a New Crystal Form of Ribonucleasea and Tetragonal Lysozyme Authors: Salunke, D.M. / Veerapandian, B. / Vijayan, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lym.cif.gz | 37.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lym.ent.gz | 28.6 KB | Display | PDB format |
PDBx/mmJSON format | 4lym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/4lym ftp://data.pdbj.org/pub/pdb/validation_reports/ly/4lym | 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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Unit cell |
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Atom site foot note | 1: THE PORTION OF THE PEPTIDE CHAIN FORMING THE LOOP (PRO 70 TO ARG 73) AND THE C-TERMINAL RESIDUES ARG 128 AND LEU 129 ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS. | |||||||||||||||||||||
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 genetically manipulated source Source: (gene. exp.) 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: 2.02 Å3/Da / Density % sol: 38.97 % | ||||||||||||||||||
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Crystal | *PLUS Density % sol: 37.8 % | ||||||||||||||||||
Crystal grow | *PLUS pH: 4.6 / Method: unknown | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 7127 / Num. measured all: 68244 / Rmerge(I) obs: 0.163 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2.1→10 Å / σ(F): 2 Details: THE PORTION OF THE PEPTIDE CHAIN FORMING THE LOOP (PRO 70 TO ARG 73) AND THE C-TERMINAL RESIDUES ARG 128 AND LEU 129 ARE CHARACTERIZED BY HIGH TEMPERATURE FACTORS.
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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