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Yorodumi- PDB-6yry: tRNA-Guanine Transglycosylase (TGT) H333A mutant crystallised at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6yry | ||||||
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Title | tRNA-Guanine Transglycosylase (TGT) H333A mutant crystallised at pH 5.5 | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / TGT / TRNA-GUANINE TRANSGLYCOSYLASE / GUANINE INSERTION ENZYME | ||||||
Function / homology | Function and homology information tRNA-guanosine34 preQ1 transglycosylase / tRNA-guanosine(34) queuine transglycosylase activity / tRNA-guanine transglycosylation / queuosine biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 Å | ||||||
Authors | Nguyen, A. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published Title: Mutation study on tRNA-guanine transglycosylase for catalysis testing Authors: Nguyen, A. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6yry.cif.gz | 110.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yry.ent.gz | 66.6 KB | Display | PDB format |
PDBx/mmJSON format | 6yry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yr/6yry ftp://data.pdbj.org/pub/pdb/validation_reports/yr/6yry | HTTPS FTP |
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-Related structure data
Related structure data | 6z0dC 1pudS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 43002.762 Da / Num. of mol.: 1 / Mutation: T312K, H333A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 (bacteria) Gene: tgt, ZMO0363 / Production host: Escherichia coli (E. coli) References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ZN / | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.95 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM MES pH 5.5, 0.5 mM DTT, 10% (v/v) DMSO, 13% (m/v) PEG8000, streak seeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Site: BESSY / Beamline: 14.1 / Type: BRUKER IMUS MICROFOCUS / Details: Incoatec microfocus source / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 17, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→44.87 Å / Num. obs: 35506 / % possible obs: 97.1 % / Redundancy: 2.9 % / Biso Wilson estimate: 23.46 Å2 / CC1/2: 0.997 / Net I/σ(I): 9.43 |
Reflection shell | Resolution: 1.82→1.93 Å / Num. unique obs: 5627 / CC1/2: 0.766 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PUD Resolution: 1.82→44.87 Å / SU ML: 0.1839 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.6445 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 26.56 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→44.87 Å
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Refine LS restraints |
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LS refinement shell |
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