+Open data
-Basic information
Entry | Database: PDB / ID: 193l | ||||||
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Title | THE 1.33 A STRUCTURE OF TETRAGONAL HEN EGG WHITE LYSOZYME | ||||||
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 / SYNCHROTRON / Resolution: 1.33 Å | ||||||
Authors | Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducruix, A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: High-resolution structure (1.33 A) of a HEW lysozyme tetragonal crystal grown in the APCF apparatus. Data and structural comparison with a crystal grown under microgravity from SpaceHab-01 mission. Authors: Vaney, M.C. / Maignan, S. / Ries-Kautt, M. / Ducriux, A. #1: Journal: To be Published Title: Effect of Microgravity on Rate of Nucleation, Size and Quality of Lysozyme Crystals Grown in the Advanced Protein Crystallization Facility on Spacehab-01 Authors: Ries-Kautt, M.M. / Broutin, I. / Ducruix, A.F. / Shephard, W. / Kahn, R. / Lorber, B. / Theobald, A. / Giege, R. / Chayen, N. / Blow, D. / Paal, K. / Littke, W. #2: Journal: J.Mol.Biol. / Year: 1994 Title: Thermal Expansion of Hen-Egg-White Lysozyme. Comparison of the 1.9 Angstroms Resolution Structures of the Tetragonal Form of the Enzyme at 100K and 298K Authors: Young, A.C.M. / Tilton, R.F. / Dewan, J.C. #3: Journal: J.Cryst.Growth / Year: 1992 Title: Experiment and Equipment for Protein Crystallization in Microgram Facilities Authors: Bosch, R. / Lautenschlager, P. / Potthast, L. / Stapelmann, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 193l.cif.gz | 37.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb193l.ent.gz | 28.4 KB | Display | PDB format |
PDBx/mmJSON format | 193l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/93/193l ftp://data.pdbj.org/pub/pdb/validation_reports/93/193l | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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 natural source / Source: (natural) Gallus gallus (chicken) / Cellular location: EGG WHITE / References: UniProt: P00698 |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-NA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.03 Å3/Da / Density % sol: 39.46 % | ||||||||||||||||||||||||
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Crystal grow | pH: 4.3 / Details: pH 4.3 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.901 Å |
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Detector | Type: MARRESEARCH / Date: Sep 1, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.901 Å / Relative weight: 1 |
Reflection | Resolution: 1.33→15 Å / Num. obs: 24111 / % possible obs: 87.1 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.031 |
Reflection | *PLUS Rmerge(I) obs: 0.031 / Biso Wilson estimate: 14.7 Å2 |
-Processing
Software |
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Refinement | Resolution: 1.33→7 Å / σ(F): 0 Details: SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG 21, ARG 61, TRP 62, ARG 73 ASN 77, LYS 97, ASP 101, ASN 103, GLN 121, ARG 125, AND LEU 129 HAVE A POORLY DEFINED DENSITY. THESE ATOMS WERE BUILT ...Details: SOME OF THE SIDE CHAIN ATOMS OF RESIDUES ARG 21, ARG 61, TRP 62, ARG 73 ASN 77, LYS 97, ASP 101, ASN 103, GLN 121, ARG 125, AND LEU 129 HAVE A POORLY DEFINED DENSITY. THESE ATOMS WERE BUILT USING STEREOCHEMICAL CONSTRAINTS AND KEPT IN THE COORDINATE FILE. WATER MOLECULES 272 AND 273 ARE ON A TWO-FOLD AXIS AND HAVE BEEN MODELED WITH 50% OCCUPANCY.
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Displacement parameters | Biso mean: 19.4 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.33→7 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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