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Yorodumi- PDB-5lyt: COMPARISON OF RADIATION-INDUCED DECAY AND STRUCTURE REFINEMENT FR... -
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-Basic information
Entry | Database: PDB / ID: 5lyt | ||||||
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Title | COMPARISON OF RADIATION-INDUCED DECAY AND STRUCTURE REFINEMENT FROM X-RAY DATA COLLECTED FROM LYSOZYME CRYSTALS AT LOW AND AMBIENT TEMPERATURES | ||||||
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: 1.9 Å | ||||||
Authors | Dewan, J.C. / Young, A.C.M. / Tilton, R.F. | ||||||
Citation | Journal: J.Appl.Crystallogr. / Year: 1993 Title: Comparison of Radiation-Induced Decay and Structure Refinement from X-Ray Data Collected from Lysozyme Crystals at Low and Ambient Temperatures Authors: Young, A.C.M. / Dewan, J.C. / Nave, C. / Tilton, R.F. #1: Journal: J.Mol.Biol. / Year: 1975 Title: An X-Ray Study of the Structure and Binding Properties of Iodine-Inactivated Lysozyme Authors: Beddell, C.R. / Blake, C.C.F. / Oatley, S.J. #2: Journal: J.Mol.Biol. / Year: 1974 Title: Real-Space Refinement of the Structure of Hen Egg-White Lysozyme Authors: Diamond, R. #3: Journal: Lysozyme / Year: 1974 Title: Crystallographic Studies of Lysozyme and its Interactions with Inhibitors and Substrates Authors: Phillips, D.C. #4: Journal: The Enzymes,Third Edition / Year: 1972 Title: Vertebrate Lysozymes Authors: Imoto, T. / Johnson, L.N. / North, A.C.T. / Phillips, D.C. / Rupley, J.A. #5: Journal: J.Mol.Biol. / Year: 1974 Title: Energy Refinement of Hen Egg-White Lysozyme Authors: Levitt, M. #6: Journal: J.Mol.Biol. / Year: 1974 Title: Crystal Structure of a Lysozyme-Tetrasaccharide Lactone Complex Authors: Ford, L.O. / Johnson, L.N. / Machin, P.A. / Phillips, D.C. / Tjian, R. #7: Journal: Proc.R.Soc.London,Ser.B / Year: 1967 Title: On the Conformation of the Hen Egg-White Lysozyme Molecule Authors: Blake, C.C.F. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R. #8: Journal: Proc.R.Soc.London,Ser.B / Year: 1967 Title: Crystallographic Studies of the Activity of Hen Egg-White Lysozyme Authors: Blake, C.C.F. / Johnson, L.N. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R. #9: Journal: Sci.Am. / Year: 1966 Title: The Three-Dimensional Structure of an Enzyme Molecule Authors: Phillips, D.C. #10: Journal: Nature / Year: 1965 Title: Structure of Hen Egg-White Lysozyme, a Three-Dimensional Fourier Synthesis at 2 Angstroms Resolution Authors: Blake, C.C.F. / Koenig, D.F. / Mair, G.A. / North, A.C.T. / Phillips, D.C. / Sarma, V.R. #11: Journal: Nature / Year: 1965 Title: Structure of Some Crystalline Lysozyme-Inhibitor Complexes Determined by X-Ray Analysis at 6 Angstroms Resolution Authors: Johnson, L.N. / Phillips, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lyt.cif.gz | 38.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lyt.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lyt_validation.pdf.gz | 415.1 KB | Display | wwPDB validaton report |
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Full document | 5lyt_full_validation.pdf.gz | 428.7 KB | Display | |
Data in XML | 5lyt_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 5lyt_validation.cif.gz | 17.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/5lyt ftp://data.pdbj.org/pub/pdb/validation_reports/ly/5lyt | HTTPS FTP |
-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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-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: 1.98 Å3/Da / Density % sol: 37.98 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 293 K / pH: 4.6 / Method: unknown | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Reflection | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 6 Å / Num. obs: 5958 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.176 |
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-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Rfactor obs: 0.176 / Highest resolution: 1.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.176 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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