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Yorodumi- PDB-5gl5: Sterol 3-beta-glucosyltransferase (ugt51) from Saccharomyces cere... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gl5 | ||||||
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Title | Sterol 3-beta-glucosyltransferase (ugt51) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c): UDPG complex | ||||||
Components | Sterol 3-beta-glucosyltransferase | ||||||
Keywords | TRANSFERASE / glycotransferase / complex / native | ||||||
Function / homology | Function and homology information sterol 3beta-glucosyltransferase / sterol 3-beta-glucosyltransferase activity / : / : / : / ascospore-type prospore membrane formation / sterol biosynthetic process / UDP-glycosyltransferase activity / sterol metabolic process / lipid glycosylation ...sterol 3beta-glucosyltransferase / sterol 3-beta-glucosyltransferase activity / : / : / : / ascospore-type prospore membrane formation / sterol biosynthetic process / UDP-glycosyltransferase activity / sterol metabolic process / lipid glycosylation / carbohydrate metabolic process / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Feng, Y. / Chen, L.-Q. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2018 Title: Structural Dissection of Sterol Glycosyltransferase UGT51 from Saccharomyces cerevisiae for Substrate Specificity. Authors: Chen, L.-Q. / Zhang, Y. / Feng, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5gl5.cif.gz | 360 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gl5.ent.gz | 290 KB | Display | PDB format |
PDBx/mmJSON format | 5gl5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gl5_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5gl5_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 5gl5_validation.xml.gz | 33.6 KB | Display | |
Data in CIF | 5gl5_validation.cif.gz | 48.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gl/5gl5 ftp://data.pdbj.org/pub/pdb/validation_reports/gl/5gl5 | HTTPS FTP |
-Related structure data
Related structure data | 5xvmC 1rrvS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 739 - 1170 / Label seq-ID: 39 - 470
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-Components
#1: Protein | Mass: 56001.094 Da / Num. of mol.: 2 / Fragment: UNP residues 722-1198 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: S288c / Gene: ATG26, UGT51, YLR189C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q06321, sterol 3beta-glucosyltransferase #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 1.94 Å3/Da / Density % sol: 36.48 % |
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Crystal grow | Temperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, magnesium chloride, Tris pH8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9202 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9202 Å / Relative weight: 1 |
Reflection | Resolution: 1.903→77.38 Å / Num. obs: 65564 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.164 / Rsym value: 0.102 / Net I/σ(I): 18.04 |
Reflection shell | Resolution: 1.903→1.97 Å / CC1/2: 0.849 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1rrv Resolution: 1.9→77.29 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.427 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.331 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→77.29 Å
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Refine LS restraints |
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