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Yorodumi- PDB-8jjq: Structure of SenB in complex with UDP-GalNAc at 1.64 Angstroms re... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8jjq | ||||||
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Title | Structure of SenB in complex with UDP-GalNAc at 1.64 Angstroms resolution | ||||||
Components | TIGR04348 family glycosyltransferase | ||||||
Keywords | TRANSFERASE / UDP-GalNAc | ||||||
Function / homology | Putative glycosyltransferase / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE / TIGR04348 family glycosyltransferase Function and homology information | ||||||
Biological species | Variovorax paradoxus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Feng, L. / Wei, H. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structure of SenB in complex with UDP-GalNAc at 1.64 Angstroms resolution Authors: Wei, H. / Feng, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8jjq.cif.gz | 218.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8jjq.ent.gz | 170.5 KB | Display | PDB format |
PDBx/mmJSON format | 8jjq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8jjq_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8jjq_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8jjq_validation.xml.gz | 47.7 KB | Display | |
Data in CIF | 8jjq_validation.cif.gz | 72.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/8jjq ftp://data.pdbj.org/pub/pdb/validation_reports/jj/8jjq | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 35325.277 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: JF629_18585 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A952K6X5 #2: Chemical | #3: 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: 3.21 Å3/Da / Density % sol: 61.63 % |
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Crystal grow | Temperature: 291.153 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 5000-MME, 0.1M Bis-Tris pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 17, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→49.99 Å / Num. obs: 157933 / % possible obs: 98.8 % / Redundancy: 6.2 % / CC1/2: 0.997 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 1.64→1.67 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6787 / CC1/2: 0.655 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→49.99 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.197 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.017 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 19.534 Å2
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Refinement step | Cycle: 1 / Resolution: 1.64→49.99 Å
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