+Open data
-Basic information
Entry | Database: PDB / ID: 7yp4 | ||||||
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Title | Crystal structure of elaiophylin glycosyltransferase in apo-form | ||||||
Components | Glycosyltransferase | ||||||
Keywords | TRANSFERASE / glycosyltransferase / elaiophylin / GT1 | ||||||
Function / homology | Function and homology information cellular glucuronidation / UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / nucleotide binding / enzyme binding Similarity search - Function | ||||||
Biological species | Streptomyces sp. SCSIO 01934 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.1 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 | 7yp4.cif.gz | 248.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7yp4.ent.gz | 199 KB | Display | PDB format |
PDBx/mmJSON format | 7yp4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7yp4_validation.pdf.gz | 472.4 KB | Display | wwPDB validaton report |
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Full document | 7yp4_full_validation.pdf.gz | 489.5 KB | Display | |
Data in XML | 7yp4_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 7yp4_validation.cif.gz | 58.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/7yp4 ftp://data.pdbj.org/pub/pdb/validation_reports/yp/7yp4 | HTTPS FTP |
-Related structure data
Related structure data | 7yp3SC 7yp5C 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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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.) Streptomyces sp. SCSIO 01934 (bacteria) Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: E5L4T5 #2: Chemical | ChemComp-PGR / #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 3.38 Å3/Da / Density % sol: 63.59 % / Mosaicity: 0.8 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.2 Details: 19% polyethylene glycol 3350, 0.15 M DL-Malic pH 7.2, 18% 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: 0.9791 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2011 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→85.47 Å / Num. obs: 36576 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.078 / Rrim(I) all: 0.161 / Net I/σ(I): 7.7 / Num. measured all: 152755 / Scaling rejects: 60 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 7YP3 Resolution: 3.1→65.69 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.894 / SU B: 23.402 / SU ML: 0.385 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.441 / 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: 268.29 Å2 / Biso mean: 86.624 Å2 / Biso min: 17.19 Å2
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Refinement step | Cycle: final / Resolution: 3.1→65.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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