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Yorodumi- PDB-1qdr: 2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOSY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qdr | ||||||
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Title | 2.1 A RESOLUTION STRUCTURE OF ESCHERICHIA COLI LYTIC TRANSGLYCOSYLASE SLT35 | ||||||
Components | LYTIC MUREIN TRANSGLYCOSYLASE B | ||||||
Keywords | HYDROLASE / ALPHA-HELICAL PROTEIN WITH AN FIVE-STRANDED ANTIPARALLEL BETA-SHEET / GLYCOSYL TRANSFERASE | ||||||
Function / homology | Function and homology information lytic endotransglycosylase activity / : / lytic transglycosylase activity / sodium ion binding / peptidoglycan catabolic process / cell wall organization / cell outer membrane / outer membrane-bounded periplasmic space / calcium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | van Asselt, E.J. / Dijkstra, A.J. | ||||||
Citation | Journal: FEBS Lett. / Year: 1999 Title: Binding of calcium in the EF-hand of Escherichia coli lytic transglycosylase Slt35 is important for stability. Authors: van Asselt, E.J. / Dijkstra, B.W. #1: Journal: To be Published / Year: 1999 Title: Crystal Structure of Escherichia Coli Lytic Transglycosylase Slt35 Reveals a Lysozyme-Like Catalytic Domain with an EF-Hand Authors: van Asselt, E.J. / Dijkstra, A.J. / Kalk, K.H. / Takacs, B. / Keck, W. / Dijkstra, B.W. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1998 Title: Accelerated X-Ray Structure Elucidation of a 36 kDa Murmidase/Transglycosylase Using Warp Authors: van Asselt, E.J. / Perrakis, A. / Kalk, K.H. / Lamzin, V.S. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qdr.cif.gz | 84.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qdr.ent.gz | 61.9 KB | Display | PDB format |
PDBx/mmJSON format | 1qdr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qd/1qdr ftp://data.pdbj.org/pub/pdb/validation_reports/qd/1qdr | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36079.660 Da / Num. of mol.: 1 / Fragment: SLT35 / Mutation: L40M, L41V Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: PERIPLASM / Cellular location (production host): PERIPLASM / Production host: Escherichia coli (E. coli) References: UniProt: P41052, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-BCN / |
#4: Chemical | ChemComp-EDO / |
#5: 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: 2.71 Å3/Da / Density % sol: 54.67 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: PEG 20K, BICINE-NAOH, ISOPROPANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.2 | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MAC Science DIP-2030 / Detector: IMAGE PLATE / Date: Nov 20, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 21174 / % possible obs: 92.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 6.2 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.19 / % possible all: 94.4 |
Reflection shell | *PLUS % possible obs: 94.4 % |
-Processing
Software |
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Refinement | Resolution: 2.1→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 16.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.17 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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