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Yorodumi- PDB-8ixq: Structure of glycosyltransferase LmbT in complex with GDP and erg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ixq | ||||||
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Title | Structure of glycosyltransferase LmbT in complex with GDP and ergothioneine | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / lincomycin / glycosyltransferase / biosynthesis / EGT | ||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / GUANOSINE-5'-DIPHOSPHATE / Chem-LW8 / LmbT Function and homology information | ||||||
Biological species | Streptomyces lincolnensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Mori, T. / Sun, X. / Abe, I. | ||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: Structure of glycosyltransferase LmbT in complex with GDP and ergothioneine Authors: Mori, T. / Sun, X. / Abe, I. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ixq.cif.gz | 441.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ixq.ent.gz | 284.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ixq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8ixq_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 8ixq_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8ixq_validation.xml.gz | 71.3 KB | Display | |
Data in CIF | 8ixq_validation.cif.gz | 106.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/8ixq ftp://data.pdbj.org/pub/pdb/validation_reports/ix/8ixq | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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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.) Streptomyces lincolnensis (bacteria) / Gene: GJU35_01490 / Production host: Escherichia coli (E. coli) / References: UniProt: A9Y8T1 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.48 % |
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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: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 16, 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: 2.1→48.82 Å / Num. obs: 126789 / % possible obs: 100 % / Redundancy: 7.7 % / Biso Wilson estimate: 22.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 8 % / Rmerge(I) obs: 0.712 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6208 / CC1/2: 1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→48.82 Å / SU ML: 0.199 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 24.6189 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: 25.13 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.82 Å
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Refine LS restraints |
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LS refinement shell |
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