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Yorodumi- PDB-4whm: Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4whm | ||||||
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Title | Crystal structure of UDP-glucose: anthocyanidin 3-O-glucosyltransferase in complex with UDP | ||||||
Components | UDP-glucose:anthocyanidin 3-O-glucosyltransferase | ||||||
Keywords | TRANSFERASE / Ct3GT-A / UGT78K6 / GT-B fold / Complexed with UDP | ||||||
Function / homology | Function and homology information UDP-glycosyltransferase activity / Transferases; Glycosyltransferases; Hexosyltransferases / nucleotide binding Similarity search - Function | ||||||
Biological species | Clitoria ternatea (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.851 Å | ||||||
Authors | Hiromoto, T. / Honjo, E. / Tamada, T. / Kuroki, R. | ||||||
Citation | Journal: Protein Sci. / Year: 2015 Title: Structural basis for acceptor-substrate recognition of UDP-glucose: anthocyanidin 3-O-glucosyltransferase from Clitoria ternatea Authors: Hiromoto, T. / Honjo, E. / Noda, N. / Tamada, T. / Kazuma, K. / Suzuki, M. / Blaber, M. / Kuroki, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4whm.cif.gz | 197.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4whm.ent.gz | 153.4 KB | Display | PDB format |
PDBx/mmJSON format | 4whm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4whm_validation.pdf.gz | 777.3 KB | Display | wwPDB validaton report |
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Full document | 4whm_full_validation.pdf.gz | 777.9 KB | Display | |
Data in XML | 4whm_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 4whm_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4whm ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4whm | HTTPS FTP |
-Related structure data
Related structure data | 4relC 4remC 4renC 3wc4S 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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-Components
#1: Protein | Mass: 48777.246 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clitoria ternatea (plant) / Gene: Ct3GT-A / Plasmid: pQE-31 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-Blue References: UniProt: A4F1R4, anthocyanidin 3-O-glucosyltransferase | ||||
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#2: Chemical | ChemComp-UDP / | ||||
#3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M ammonium acetate, 26%(w/v) PEG 4000, 0.1M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 38569 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 16.45 Å2 / Rmerge(I) obs: 0.083 / Χ2: 0.915 / Net I/av σ(I): 15.2 / Net I/σ(I): 8.8 / Num. measured all: 142408 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3WC4 Resolution: 1.851→26.235 Å / FOM work R set: 0.8926 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.71 Å2 / Biso mean: 16.48 Å2 / Biso min: 4.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.851→26.235 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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