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Open data
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Basic information
Entry | Database: PDB / ID: 8ixp | ||||||
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Title | Apo structure of glycosyltransferase LmbT wild type | ||||||
![]() | Glycosyltransferase | ||||||
![]() | TRANSFERASE / lincomycin / glycosyltransferase / biosynthesis | ||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / LmbT![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Mori, T. / Sun, X. / Abe, I. | ||||||
Funding support | 1items
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![]() | ![]() Title: Apo structure of glycosyltransferase LmbT wild type Authors: Mori, T. / Sun, X. / Abe, I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 324.3 KB | Display | ![]() |
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PDB format | ![]() | 259.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 457.9 KB | Display | ![]() |
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Full document | ![]() | 471.3 KB | Display | |
Data in XML | ![]() | 57.6 KB | Display | |
Data in CIF | ![]() | 81.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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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: 48909.164 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.03M citrate acid, 0.07M BIS-tris propane pH7.6, 28% Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→48.77 Å / Num. obs: 81741 / % possible obs: 100 % / Redundancy: 13.6 % / Biso Wilson estimate: 39.14 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.155 / Net I/σ(I): 12.8 |
Reflection shell | Resolution: 2.45→2.5 Å / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4453 / CC1/2: 0.879 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.07 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→48.77 Å
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Refine LS restraints |
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LS refinement shell |
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