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- PDB-1sly: COMPLEX OF THE 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE WITH BULGECIN A -
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Open data
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Basic information
Entry | Database: PDB / ID: 1sly | ||||||
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Title | COMPLEX OF THE 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE WITH BULGECIN A | ||||||
![]() | 70-KDA SOLUBLE LYTIC TRANSGLYCOSYLASE | ||||||
![]() | GLYCOSYLTRANSFERASE / INHIBITOR-ENZYME COMPLEX / LYSOZYME / PEPTIDOGLYCAN / HYDROLASE / GLYCOSIDASE / PERIPLASMIC | ||||||
Function / homology | ![]() lytic endotransglycosylase activity / : / lytic transglycosylase activity / peptidoglycan metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / peptidoglycan-based cell wall / cell wall organization / outer membrane-bounded periplasmic space / periplasmic space ...lytic endotransglycosylase activity / : / lytic transglycosylase activity / peptidoglycan metabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / peptidoglycan-based cell wall / cell wall organization / outer membrane-bounded periplasmic space / periplasmic space / lyase activity / membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Thunnissen, A.M.W.H. / Kalk, K.H. / Rozeboom, H.J. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: Structure of the 70-kDa soluble lytic transglycosylase complexed with bulgecin A. Implications for the enzymatic mechanism. Authors: Thunnissen, A.M. / Rozeboom, H.J. / Kalk, K.H. / Dijkstra, B.W. #1: ![]() Title: The Catalytic Domain of a Bacterial Lytic Transglycosylase Defines a Novel Class of Lysozymes Authors: Thunnissen, A.M. / Isaacs, N.W. / Dijkstra, B.W. #2: ![]() Title: 'Holy' Proteins. II: The Soluble Lytic Transglycosylase Authors: Dijkstra, B.W. / Thunnissen, A.M. #3: ![]() Title: Doughnut-Shaped Structure of a Bacterial Muramidase Revealed by X-Ray Crystallography Authors: Thunnissen, A.M. / Dijkstra, A.J. / Kalk, K.H. / Rozeboom, H.J. / Engel, H. / Keck, W. / Dijkstra, B.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.5 KB | Display | ![]() |
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PDB format | ![]() | 105.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.1 KB | Display | ![]() |
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Full document | ![]() | 471.8 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 21.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 70560.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P03810, UniProt: P0AGC3*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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#2: Chemical | ChemComp-BLG / |
Compound details | THE STRUCTURE CONSISTS OF 3 DOMAINS: DOMAIN RESIDUES COMMENT U 1 - 361 ALPHA-SUPERHELIX TOPOLOGY L ...THE STRUCTURE CONSISTS OF 3 DOMAINS: DOMAIN RESIDUES COMMENT U 1 - 361 ALPHA-SUPERHELIX |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.2 % | |||||||||||||||||||||||||
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Crystal | *PLUS Density % sol: 63 % | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.8 / Method: vapor diffusion, hanging drop / Details: Rozeboom, H. J., (1990) J. Mol. Biol., 212, 557. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: ![]() ![]() ![]() |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 20, 1993 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.003 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→22 Å / Num. obs: 23903 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.08 |
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Processing
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Refinement | Resolution: 2.8→8 Å / σ(F): 2 Details: RESIDUES 371 - 377 ARE POORLY DEFINED BY THE ELECTRON DENSITY. THESE RESIDUES BELONG TO A LONG SURFACE LOOP THAT CONNECTS THE U- AND L-DOMAINS.
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Displacement parameters | Biso mean: 24.15 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å / Luzzati sigma a obs: 0.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Num. reflection obs: 22746 / Rfactor obs: 0.195 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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