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Yorodumi- PDB-6z0d: tRNA-Guanine Transglycosylase (TGT) H333F mutant crystallised at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6z0d | ||||||
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Title | tRNA-Guanine Transglycosylase (TGT) H333F 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 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 / MOLECULAR REPLACEMENT / Resolution: 1.65 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 | 6z0d.cif.gz | 115.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z0d.ent.gz | 70 KB | Display | PDB format |
PDBx/mmJSON format | 6z0d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/6z0d ftp://data.pdbj.org/pub/pdb/validation_reports/z0/6z0d | HTTPS FTP |
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-Related structure data
Related structure data | 6yryC 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: 43078.855 Da / Num. of mol.: 1 / Mutation: T312K, H333F 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: 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: 2.59 Å3/Da / Density % sol: 52.48 % |
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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 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 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: 1.65→40 Å / Num. obs: 47815 / % possible obs: 96.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 15.25 Å2 / CC1/2: 0.999 / Net I/σ(I): 22.25 |
Reflection shell | Resolution: 1.65→1.75 Å / Num. unique obs: 6664 / CC1/2: 0.991 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1PUD Resolution: 1.65→40 Å / SU ML: 0.2716 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2131
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→40 Å
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Refine LS restraints |
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LS refinement shell |
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