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Yorodumi- PDB-2nqz: Trna-guanine transglycosylase (TGT) mutant in complex with 7-deaz... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2nqz | ||||||
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Title | Trna-guanine transglycosylase (TGT) mutant in complex with 7-deaza-7-aminomethyl-guanine | ||||||
Components | Queuine tRNA-ribosyltransferase | ||||||
Keywords | TRANSFERASE / TGT / preQ1 | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Tidten, N. / Heine, A. / Reuter, K. / Klebe, G. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Investigation of Specificity Determinants in Bacterial tRNA-Guanine Transglycosylase Reveals Queuine, the Substrate of Its Eucaryotic Counterpart, as Inhibitor Authors: Biela, I. / Tidten-Luksch, N. / Immekus, F. / Glinca, S. / Nguyen, T.X. / Gerber, H.D. / Heine, A. / Klebe, G. / Reuter, K. | ||||||
History |
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Remark 999 | SEQUENCE See Ref. 1 and 2 in the sequence database, TGT_ZYMMO. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2nqz.cif.gz | 166.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2nqz.ent.gz | 128.8 KB | Display | PDB format |
PDBx/mmJSON format | 2nqz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nq/2nqz ftp://data.pdbj.org/pub/pdb/validation_reports/nq/2nqz | HTTPS FTP |
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-Related structure data
Related structure data | 2nsoC 3bl3C 3bldC 3bllC 3bloC 4e2vC 4gcxC 4gd0C 4h6eC 4h7zC 4hqvC 4hshC 4hvxC 1y5xS 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: 42748.418 Da / Num. of mol.: 1 / Mutation: Y106F, C158V, A232S, V233G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis (bacteria) / Gene: tgt / Plasmid: pET-9d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||
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#2: Chemical | ChemComp-ZN / | ||||
#3: Chemical | ChemComp-PRF / | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | See Ref. 1 and 2 in the sequence database, TGT_ZYMMO. | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.02 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 100mM Tris/HCl, 1mM DTT, 5% PEG 8000, 10% DMSO, 14mg/ml TGT, 20mM preQ1, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 16, 2004 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→20 Å / Num. all: 64991 / Num. obs: 64991 / % possible obs: 98.6 % / Redundancy: 3.2 % / Rsym value: 0.044 / Net I/σ(I): 18 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Y5X Resolution: 1.46→8 Å / Num. parameters: 31725 / Num. restraintsaints: 39887 / Isotropic thermal model: ANISOTROPIC / Cross valid method: FREE R Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Solvent computation | Solvent model: BABINET (SWAT) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 31 / Occupancy sum hydrogen: 2827 / Occupancy sum non hydrogen: 3365 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.46→8 Å
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Refine LS restraints |
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