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- PDB-2nso: Trna-gunanine-transglycosylase (TGT) mutant Y106F, C158V, A232S, ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2nso | ||||||
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Title | Trna-gunanine-transglycosylase (TGT) mutant Y106F, C158V, A232S, V233G- APO-Structure | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / TRNA-GUNANINE-TRANSGLYCOSYLASE (TGT) | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Tidten, N. / Heine, A. / Reuter, K. / Klebe, G. | ||||||
![]() | ![]() 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 UNIPROT SEQUENCE DATABASE, TGT_ZYMMO. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 160.9 KB | Display | ![]() |
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PDB format | ![]() | 124.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 437.8 KB | Display | ![]() |
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Full document | ![]() | 441.5 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 24.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2nqzC ![]() 3bl3C ![]() 3bldC ![]() 3bllC ![]() 3bloC ![]() 4e2vC ![]() 4gcxC ![]() 4gd0C ![]() 4h6eC ![]() 4h7zC ![]() 4hqvC ![]() 4hshC ![]() 4hvxC ![]() 1y5xS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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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Details | The second part of the biological assembly is generated by the two fold axis |
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Components
#1: Protein | Mass: 42879.613 Da / Num. of mol.: 1 / Mutation: Y106F, C158V, A232S, V233G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||
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#2: Chemical | ChemComp-ZN / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.48 % |
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Crystal grow | pH: 8.5 Details: 100 mM Tris/HCl, 1 mM DTT, 5% PEG 8000, 10% DMSO, pH 8.50 |
-Data collection
Diffraction source | Source: ![]() |
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Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 13, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 53101 / % possible obs: 98.6 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.1331 / Rsym value: 0.071 / Net I/σ(I): 15 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Y5X Resolution: 1.6→28.42 Å / Num. parameters: 29645 / Num. restraintsaints: 36523 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER 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).
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Solvent computation | Solvent model: BABINET (SWAT) | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 3 / Occupancy sum hydrogen: 2815 / Occupancy sum non hydrogen: 3240.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→28.42 Å
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Refine LS restraints |
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