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Yorodumi- PDB-5lym: STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMEN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lym | |||||||||
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Title | STUDIES OF MONOCLINIC HEN EGG WHITE LYSOZYME. IV. X-RAY REFINEMENT AT 1.8 ANGSTROM RESOLUTION AND A COMPARISON OF THE VARIABLE REGIONS IN THE POLYMORPHIC FORMS | |||||||||
Components | 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: 1.8 Å | |||||||||
Authors | Rao, S.T. / Sundaralingam, M. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Studies of monoclinic hen egg-white lysozyme. IV. X-ray refinement at 1.8 A resolution and a comparison of the variable regions in the polymorphic forms. Authors: Rao, S.T. / Sundaralingam, M. #1: Journal: To be Published Title: X-Ray Refinement Studies on Monoclinic Hel Containing Two Independent Molecules at 1.8 Angstrom Resolution Authors: Yu, C. / Rao, S.T. / Sundaralingam, M. #2: Journal: Acta Crystallogr.,Sect.C / Year: 1983 Title: Studies of Monoclinic Hen Egg White Lysozyme. II. The Refinement at 2.5 Angstroms Resolution-Conformational Variability between the Two Independent Molecules Authors: Rao, S.T. / Hogle, J. / Sundaralingam, M. #3: Journal: Acta Crystallogr.,Sect.B / Year: 1981 Title: Studies of Monoclinic Hen Egg White Lysozyme. I. Structure Solution at 4 Angstroms Resolution and Molecular-Packing Comparisons with Tetragonal and Triclinic Lysozymes Authors: Hogle, J. / Rao, S.T. / Mallikarjunan, M. / Beddell, C. / Mcmullan, R.K. / Sundaralingam, M. #4: Journal: Thesis / Year: 1978 Title: The Structure of the Monoclinic Crystal Form of Hen Egg White Lysozyme at 2.5 Angstroms Resolution. Comparison of a Protein Structure in Several Crystalline Environments Authors: Hogle, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lym.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lym.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 5lym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ly/5lym ftp://data.pdbj.org/pub/pdb/validation_reports/ly/5lym | 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: (0.9738, -0.1931, 0.1201), Vector: |
-Components
#1: Protein | Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Cell: EGG WHITE / References: UniProt: P00698, lysozyme #2: Chemical | ChemComp-NO3 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.86 Å3/Da / Density % sol: 33.82 % |
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Crystal grow | *PLUS Method: other / Details: Hogle, J., (1981) Acta Cryst., B37, 591. |
-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: BRUKER NONIUS CAD4 / Detector: DIFFRACTOMETER |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→8 Å / Num. obs: 18822 / % possible obs: 99 % |
Reflection | *PLUS Observed criterion σ(I): 0 |
-Processing
Software |
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Refinement | Resolution: 1.8→8 Å / σ(F): 3
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Displacement parameters | Biso mean: 19.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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