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Yorodumi- PDB-7yp5: Crystal structure of elaiophylin glycosyltransferase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7yp5 | ||||||
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Title | Crystal structure of elaiophylin glycosyltransferase in complex with TDP | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase / elaiophylin / GT1 | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process Similarity search - Function | ||||||
Biological species | Streptomyces sp. SCSIO 01934 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 Å | ||||||
Authors | Xu, T. / Liu, Q. / Gan, Q. / Liu, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2022 Title: Substrate-induced dimerization of elaiophylin glycosyltransferase reveals a novel self-activating form of glycosyltransferase for symmetric glycosylation. Authors: Xu, T. / Gan, Q. / Liu, Q. / Chen, R. / Zhen, X. / Zhang, C. / Liu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7yp5.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yp5.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 7yp5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/7yp5 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7yp5 | HTTPS FTP |
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-Related structure data
Related structure data | 7yp3SC 7yp4C 7yp6C S: Starting model for refinement 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: 48544.961 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. SCSIO 01934 (bacteria) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5L4T5 #2: Chemical | #3: Chemical | ChemComp-PGR / #4: Chemical | ChemComp-CL / | #5: 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: 3.13 Å3/Da / Density % sol: 60.72 % / Mosaicity: 1.04 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.2 Details: 22% polyethylene glycol 3350, 0.15 M DL-Malic pH 7.2, 25% propylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 8, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→95.28 Å / Num. obs: 50754 / % possible obs: 95.1 % / Redundancy: 24.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.043 / Rrim(I) all: 0.219 / Net I/σ(I): 10.2 / Num. measured all: 1240470 / Scaling rejects: 1540 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7YP3 Resolution: 2.33→75.21 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.83 / SU ML: 0.194 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.294 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 161.05 Å2 / Biso mean: 49.41 Å2 / Biso min: 22.83 Å2
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Refinement step | Cycle: final / Resolution: 2.33→75.21 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.33→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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