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- PDB-1qsa: CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SL... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1qsa | ||||||
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Title | CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 FROM ESCHERICHIA COLI AT 1.65 ANGSTROMS RESOLUTION | ||||||
![]() | PROTEIN (SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70) | ||||||
![]() | TRANSFERASE / ALPHA-SUPERHELIX | ||||||
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 | ![]() ![]() | ||||||
![]() | van Asselt, E.J. / Thunnissen, A.-M.W.H. / Dijkstra, B.W. | ||||||
![]() | ![]() Title: High resolution crystal structures of the Escherichia coli lytic transglycosylase Slt70 and its complex with a peptidoglycan fragment. Authors: van Asselt, E.J. / Thunnissen, A.M. / 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 | ![]() | 157.8 KB | Display | ![]() |
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PDB format | ![]() | 130.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.4 KB | Display | ![]() |
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Full document | ![]() | 445.7 KB | Display | |
Data in XML | ![]() | 32.8 KB | Display | |
Data in CIF | ![]() | 53.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 70544.516 Da / Num. of mol.: 1 / Fragment: FULL PROTEIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() 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-SO4 / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 Details: SODIUM ACETATE, AMMONIUM SULFATE, SODIUM AZIDE, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
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 | Mean temperature: 120 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PRINCETON 2K / Detector: CCD / Date: Apr 9, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→34 Å / Num. all: 335588 / Num. obs: 100894 / % possible obs: 92.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 23 |
Reflection shell | Resolution: 1.65→1.68 Å / Redundancy: 2 % / Rmerge(I) obs: 0.255 / % possible all: 75.6 |
Reflection | *PLUS Num. measured all: 335588 |
Reflection shell | *PLUS % possible obs: 75.6 % |
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Processing
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Refinement | Resolution: 1.65→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME USED BULK SOLVENT MODEL USED, ANISOTROPIC B-FACTOR SCALING USED,
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Displacement parameters | Biso mean: 20.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 12
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.254 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.217 |