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- PDB-2qii: Crystal Structure Of tRNA-Guanine Transglycosylase (TGT) From Zym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qii | ||||||
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Title | Crystal Structure Of tRNA-Guanine Transglycosylase (TGT) From Zymomonas mobilis Complexed With Archaeosine Precursor, Preq0 | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE | ||||||
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. / Brenk, R. / Heine, A. / Reuter, K. / Klebe, G. | ||||||
![]() | ![]() Title: Glutamate versus glutamine exchange swaps substrate selectivity in tRNA-guanine transglycosylase: insight into the regulation of substrate selectivity by kinetic and crystallographic studies. Authors: Tidten, N. / Stengl, B. / Heine, A. / Garcia, G.A. / Klebe, G. / Reuter, K. | ||||||
History |
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Remark 999 | SEQUENCE There is a conflict at residue 312 (Thr > Lys) in the UNP entry P28720 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 70.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.5 KB | Display | ![]() |
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Full document | ![]() | 466.4 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2okoC ![]() 2potC ![]() 2pwuC ![]() 2pwvC ![]() 2z1vC ![]() 2z1wC ![]() 2z1xC ![]() 1p0bS 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: 42925.703 Da / Num. of mol.: 1 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 | ChemComp-PQ0 / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.09 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, MES, DMSO, DTT, preQ0, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 113 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 6, 2003 |
Radiation | Monochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 43081 / Num. obs: 43081 / % possible obs: 95.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.1 Å2 |
Reflection shell | Resolution: 1.7→1.73 Å / Rsym value: 0.562 / % possible all: 92.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1p0b Resolution: 1.7→20 Å / Num. parameters: 13071 / Num. restraintsaints: 12439 / 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
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Refine analyze | Num. disordered residues: 12 / Occupancy sum hydrogen: 2794 / Occupancy sum non hydrogen: 3195.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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