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Yorodumi- PDB-6ygv: tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ygv | ||||||
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Title | tRNA-Guanine Transglycosylase (TGT) in co-crystallized complex with (E)-N-ethyl-4-oxo-4-phenylbut-2-enamide | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME / HOMODIMER | ||||||
Function / homology | Function and homology information tRNA-guanosine34 preQ1 transglycosylase / tRNA wobble guanine modification / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Zymomonas mobilis subsp. mobilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å | ||||||
Authors | Nguyen, A. / Heyder, L. / Heine, A. / Diederich, W. / Klebe, G. | ||||||
Citation | Journal: To Be Published Title: Ligands disturb dimer contacts Authors: Nguyen, A. / Heyder, L. / Heine, A. / Diederich, W. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ygv.cif.gz | 278.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ygv.ent.gz | 187.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ygv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ygv_validation.pdf.gz | 688.7 KB | Display | wwPDB validaton report |
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Full document | 6ygv_full_validation.pdf.gz | 688.7 KB | Display | |
Data in XML | 6ygv_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 6ygv_validation.cif.gz | 26.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yg/6ygv ftp://data.pdbj.org/pub/pdb/validation_reports/yg/6ygv | HTTPS FTP |
-Related structure data
Related structure data | 1pudS 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: 42910.605 Da / Num. of mol.: 1 / Mutation: T312K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4) (bacteria) Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-OQH / ~{ | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.43 Å3/Da / Density % sol: 49.36 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 100 mM TRIS pH 8.5, 20% (m/v) PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2019 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.63→45.19 Å / Num. obs: 50766 / % possible obs: 99.5 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.03 Å2 / CC1/2: 1 / Net I/σ(I): 25.55 |
Reflection shell | Resolution: 1.63→1.73 Å / Num. unique obs: 8139 / CC1/2: 0.908 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PUD Resolution: 1.63→45.19 Å / SU ML: 0.1404 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.8692
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.63→45.19 Å
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Refine LS restraints |
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LS refinement shell |
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