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- PDB-1qte: 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: 1qte | ||||||
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Title | CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 FROM ESCHERICHIA COLI AT 1.90 A RESOLUTION IN COMPLEX WITH A 1,6-ANHYDROMUROTRIPEPTIDE | ||||||
![]() | SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 | ||||||
![]() | HYDROLASE / ALPHA-SUPERHELIX | ||||||
Function / homology | ![]() lytic endotransglycosylase activity / : / lytic transglycosylase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / peptidoglycan catabolic process / peptidoglycan-based cell wall / cell wall organization / outer membrane-bounded periplasmic space / 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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PDBx/mmCIF format | ![]() | 155 KB | Display | ![]() |
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PDB format | ![]() | 124.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 882.5 KB | Display | ![]() |
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Full document | ![]() | 883.6 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 51.9 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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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 70544.516 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH 1,6-ANHYDROMUROTRIPEPTIDE, DAL-ALA-AH0 Source: (gene. exp.) ![]() ![]() ![]() ![]() References: PIR: S56616, UniProt: P0AGC3*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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#2: Sugar | ChemComp-NAG / |
-Non-polymers , 7 types, 895 molecules ![](data/chem/img/SO4.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/DAL.gif)
![](data/chem/img/AH0.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/ALA.gif)
![](data/chem/img/DAL.gif)
![](data/chem/img/AH0.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-ALA / | #6: Chemical | ChemComp-DAL / | #7: Chemical | ChemComp-AH0 / | #8: Chemical | ChemComp-GOL / #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.87 % | ||||||||||||||||||||||||||||||
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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: 1.9→15 Å / Num. obs: 57525 / % possible obs: 79.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.9 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.148 / % possible all: 64.6 |
Reflection | *PLUS Num. measured all: 193873 |
Reflection shell | *PLUS % possible obs: 63.7 % |
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Processing
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Refinement | Resolution: 1.9→15 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER Details: USED RESOLUTION-DEPENDENT WEIGHTING SCHEME, BULK SOLVENT MODEL, AND ANISOTROPIC B-FACTOR SCALING
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Displacement parameters | Biso mean: 25.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.96 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 12
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Refinement | *PLUS Lowest resolution: 15 Å / Num. reflection obs: 56504 / Rfactor obs: 0.172 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.22 |