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Yorodumi- PDB-6pnt: Structural Characterization of UDP-glycosyltransferase from Tetra... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pnt | ||||||
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Title | Structural Characterization of UDP-glycosyltransferase from Tetranychus Urticae | ||||||
Components | UDP-glycosyltransferase 202A2 | ||||||
Keywords | TRANSFERASE / Uridine diphosphate / UDP-glycosyltransferase / Two-spotted Spider Mite / Pesticide detoxification | ||||||
Function / homology | : / UDP-glycosyltransferase activity / UDP-glucoronosyl and UDP-glucosyl transferase / UDP-glucuronosyl/UDP-glucosyltransferase / nucleotide binding / membrane / UDP-glycosyltransferase 202A2 Function and homology information | ||||||
Biological species | Tetranychus urticae (two-spotted spider mite) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Daneshian, L. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M. | ||||||
Citation | Journal: To Be Published Title: Structural Characterization of UDP-glycosyltransferase from Tetranychus Urticae Authors: Daneshian, L. / Dermauw, W. / Wybouw, N. / Van Leeuwen, T. / Chruszcz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pnt.cif.gz | 186.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pnt.ent.gz | 147.1 KB | Display | PDB format |
PDBx/mmJSON format | 6pnt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pnt_validation.pdf.gz | 415.3 KB | Display | wwPDB validaton report |
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Full document | 6pnt_full_validation.pdf.gz | 415.6 KB | Display | |
Data in XML | 6pnt_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6pnt_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/6pnt ftp://data.pdbj.org/pub/pdb/validation_reports/pn/6pnt | HTTPS FTP |
-Related structure data
Related structure data | 2iyaS S: Starting model for refinement |
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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: 48950.504 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tetranychus urticae (two-spotted spider mite) Gene: 107367435, UGT202A2 / Plasmid: pET100/D-TOPO / Production host: Escherichia coli (E. coli) / References: UniProt: T1KUK4 |
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#2: 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: 2.38 Å3/Da / Density % sol: 48.21 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% Tacsimate pH 7.0, 0.1 M HEPES pH 7.0, 10% PEG 5000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→40 Å / Num. obs: 39554 / % possible obs: 99.3 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.032 / Rrim(I) all: 0.09 / Rsym value: 0.083 / Net I/σ(I): 33.32 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.627 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1947 / CC1/2: 0.731 / Rpim(I) all: 0.267 / Rrim(I) all: 0.684 / Rsym value: 0.627 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IYA Resolution: 1.85→29.88 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.124 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 84.23 Å2 / Biso mean: 31.231 Å2 / Biso min: 19.86 Å2
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Refinement step | Cycle: final / Resolution: 1.85→29.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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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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