[English] 日本語
Yorodumi- PDB-1qsa: CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qsa | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF THE 70 KDA SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70 FROM ESCHERICHIA COLI AT 1.65 ANGSTROMS RESOLUTION | ||||||
Components | PROTEIN (SOLUBLE LYTIC TRANSGLYCOSYLASE SLT70) | ||||||
Keywords | TRANSFERASE / ALPHA-SUPERHELIX | ||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 Å | ||||||
Authors | van Asselt, E.J. / Thunnissen, A.-M.W.H. / Dijkstra, B.W. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1qsa.cif.gz | 157.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1qsa.ent.gz | 130.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qsa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qs/1qsa ftp://data.pdbj.org/pub/pdb/validation_reports/qs/1qsa | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) References: UniProt: P03810, UniProt: P0AGC3*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.21 Å3/Da / Density % sol: 61.72 % | ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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
|
-Data collection
Diffraction | Mean temperature: 120 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.92 |
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 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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,
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.7 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 12
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 20.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.254 / % reflection Rfree: 10.8 % / Rfactor Rwork: 0.217 |