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Yorodumi- PDB-8il0: Crystal structure of LmbT from Streptomyces lincolnensis NRRL ISP-5355 -
+Open data
-Basic information
Entry | Database: PDB / ID: 8il0 | |||||||||
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Title | Crystal structure of LmbT from Streptomyces lincolnensis NRRL ISP-5355 | |||||||||
Components | Glycosyltransferase | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / Glycosyltransferase | |||||||||
Function / homology | Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / LmbT Function and homology information | |||||||||
Biological species | Streptomyces lincolnensis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å | |||||||||
Authors | Dai, Y. / Li, P. / Qiao, H. / Xia, M. / Liu, W. / Fang, P. | |||||||||
Funding support | China, 2items
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Citation | Journal: Acs Chem.Biol. / Year: 2023 Title: Structural Basis of Low-Molecular-Weight Thiol Glycosylation in Lincomycin A Biosynthesis. Authors: Dai, Y. / Cheng, Y. / Ding, W. / Qiao, H. / Zhang, D. / Zhong, G. / Xia, M. / Tao, J. / Sun, P. / Fang, P. / Liu, W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8il0.cif.gz | 172.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8il0.ent.gz | 137.1 KB | Display | PDB format |
PDBx/mmJSON format | 8il0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8il0_validation.pdf.gz | 432.9 KB | Display | wwPDB validaton report |
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Full document | 8il0_full_validation.pdf.gz | 440.6 KB | Display | |
Data in XML | 8il0_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 8il0_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/il/8il0 ftp://data.pdbj.org/pub/pdb/validation_reports/il/8il0 | HTTPS FTP |
-Related structure data
Related structure data | 8ilaC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 49408.723 Da / Num. of mol.: 1 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 |
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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: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M Magnesium acetate tetrahydrate, 0.1 M MES, pH6.5 10 %, w/v PEG 10000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979021 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979021 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→91.82 Å / Num. obs: 12924 / % possible obs: 95.3 % / Redundancy: 10 % / CC1/2: 0.999 / Net I/σ(I): 23 |
Reflection shell | Resolution: 2.81→2.96 Å / Num. unique obs: 1925 / CC1/2: 0.831 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.81→49.31 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.68 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.81→49.31 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 22.9425 Å / Origin y: -2.6882 Å / Origin z: 19.8275 Å
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Refinement TLS group | Selection details: all |