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- PDB-7yp6: Crystal structure of elaiophylin glycosyltransferase in complex w... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yp6 | ||||||
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Title | Crystal structure of elaiophylin glycosyltransferase in complex with UDP | ||||||
![]() | Glycosyltransferase | ||||||
![]() | TRANSFERASE / glycosyltransferase / elaiophylin / GT1 | ||||||
Function / homology | ![]() cellular glucuronidation / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / nucleotide binding / enzyme binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, T. / Liu, Q. / Gan, Q. / Liu, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 253.5 KB | Display | ![]() |
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PDB format | ![]() | 202.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 45 KB | Display | |
Data in CIF | ![]() | 62.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7yp3SC ![]() 7yp4C ![]() 7yp5C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 48544.961 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Plasmid: pET28a / Production host: ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-PGR / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.71 % / Mosaicity: 0.7 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.2 Details: 21% polyethylene glycol 3350, 0.15 M DL-Malic pH 7.2, 24% propylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2010 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.6→65.23 Å / Num. obs: 62124 / % possible obs: 99.9 % / Redundancy: 4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.059 / Rrim(I) all: 0.12 / Net I/σ(I): 8.4 / Num. measured all: 249252 / Scaling rejects: 65 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7YP3 Resolution: 2.6→64.12 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.59 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.389 / ESU R Free: 0.265 / 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: 256.45 Å2 / Biso mean: 75.334 Å2 / Biso min: 27.52 Å2
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Refinement step | Cycle: final / Resolution: 2.6→64.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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