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Yorodumi- PDB-1lsp: THE CRYSTAL STRUCTURE OF A BULGECIN-INHIBITED G-TYPE LYSOZYME FRO... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1lsp | ||||||
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Title | THE CRYSTAL STRUCTURE OF A BULGECIN-INHIBITED G-TYPE LYSOZYME FROM THE EGG-WHITE OF THE AUSTRALIAN BLACK SWAN. A COMPARISON OF THE BINDING OF BULGECIN TO THREE MURAMIDASES | ||||||
Components | LYSOZYME | ||||||
Keywords | HYDROLASE (O-GLYCOSYL) | ||||||
Function / homology | Function and homology information peptidoglycan catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region Similarity search - Function | ||||||
Biological species | Cygnus atratus (black swan) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.45 Å | ||||||
Authors | Karlsen, S. / Rao, Z.H. / Hough, E. / Isaacs, N.W. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 1996 Title: Structure of a bulgecin-inhibited g-type lysozyme from the egg white of the Australian black swan. A comparison of the binding of bulgecin to three muramidases. Authors: Karlsen, S. / Hough, E. / Rao, Z.H. / Isaacs, N.W. #1: Journal: To be Published Title: The Crystal Structure of a Complex between Bulgecin, a Bacterial Metabolite, and Lysozyme from the Rainbow Trout Authors: Karlsen, S. / Hough, E. #2: Journal: Aust.J.Biol.Sci. / Year: 1985 Title: Three-Dimensional Structure of Goose-Type Lysozyme from the Egg White of the Australian Black Swan, Cygnus Atratus Authors: Isaacs, N.W. / Machin, K.J. / Masakuni, M. #3: Journal: Tetrahedron / Year: 1984 Title: Structures of Bulgecins, Bacterial Metabolites with Bulge-Inducing Activity Authors: Shinagawa, S. / Kasahara, F. / Wada, Y. / Harada, S. / Asai, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lsp.cif.gz | 47.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lsp.ent.gz | 36.8 KB | Display | PDB format |
PDBx/mmJSON format | 1lsp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1lsp_validation.pdf.gz | 656.6 KB | Display | wwPDB validaton report |
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Full document | 1lsp_full_validation.pdf.gz | 668.8 KB | Display | |
Data in XML | 1lsp_validation.xml.gz | 8.4 KB | Display | |
Data in CIF | 1lsp_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ls/1lsp ftp://data.pdbj.org/pub/pdb/validation_reports/ls/1lsp | 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: 20434.172 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cygnus atratus (black swan) / Cellular location: EGG WHITE / References: UniProt: P00717, lysozyme |
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#2: Chemical | ChemComp-BUL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 55.99 % | ||||||||||||||||||
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Crystal grow | *PLUS pH: 6.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 Å |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jun 1, 1994 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Num. obs: 6959 / % possible obs: 78.9 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.055 |
Reflection | *PLUS Highest resolution: 2.45 Å / Lowest resolution: 32.94 Å |
-Processing
Software |
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Refinement | Resolution: 2.45→8 Å / σ(F): 3 /
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Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→8 Å
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Refine LS restraints |
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