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Yorodumi- PDB-2lzt: REFINEMENT OF TRICLINIC LYSOZYME. II. THE METHOD OF STEREOCHEMICA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lzt | ||||||
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Title | REFINEMENT OF TRICLINIC LYSOZYME. II. THE METHOD OF STEREOCHEMICALLY RESTRAINED LEAST-SQUARES | ||||||
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: 1.97 Å | ||||||
Authors | Ramanadham, M. / Sieker, L.C. / Jensen, L.H. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.B / Year: 1990 Title: Refinement of triclinic lysozyme: II. The method of stereochemically restrained least squares. Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H. #1: Journal: To be Published Title: Refinement of Triclinic Lysozyme. I. Fourier and Least Squares Methods Authors: Hodsdon, J.M. / Brown, G.M. / Sieker, L.C. / Jensen, L.H. #2: Journal: The Immune Response to Structurally Defined Proteins. The Lysozyme Model Year: 1989 Title: Triclinic Lysozyme. Some Features of the Structure at 2 Angstroms Resolution Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H. #3: Journal: Acta Crystallogr.,Sect.A / Year: 1987 Title: Srlsq Refinement of Triclinic Lysozyme Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H. #4: Journal: Acta Crystallogr.,Sect.A / Year: 1981 Title: Structure of Triclinic Lysozyme and its Cu2+ Complex at 2 Angstroms Resolution Authors: Ramanadham, M. / Sieker, L.C. / Jensen, L.H. #5: Journal: J.Mol.Biol. / Year: 1976 Title: Structures of Triclinic Mono-and Di-N-Acetylglucosamine. Lysozyme Complexes-A Crystallographic Study Authors: Kurachi, K. / Sieker, L.C. / Jensen, L.H. #6: Journal: J.Biol.Chem. / Year: 1975 Title: Metal Ion Binding in Triclinic Lysozyme Authors: Kurachi, K. / Sieker, L.C. / Jensen, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lzt.cif.gz | 39.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lzt.ent.gz | 30.6 KB | Display | PDB format |
PDBx/mmJSON format | 2lzt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lz/2lzt ftp://data.pdbj.org/pub/pdb/validation_reports/lz/2lzt | 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: SEE REMARK 5. |
-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: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.65 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4.55 / Method: unknownDetails: taken from Kurachi, K. et al (1976). J. Mol. Biol., 101-11-24. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.97 Å / Lowest resolution: 9999 Å / Num. obs: 7075 / Rmerge(I) obs: 0.314 / Biso Wilson estimate: 8 Å2 / Num. measured all: 7131 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.124 / Highest resolution: 1.97 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.97 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.97 Å / Rfactor obs: 0.124 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |