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- PDB-1k4g: CRYSTAL STRUCTURE OF TRNA-GUANINE TRANSGLYCOSYLASE (TGT) COMPLEXE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k4g | ||||||
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Title | CRYSTAL STRUCTURE OF TRNA-GUANINE TRANSGLYCOSYLASE (TGT) COMPLEXED WITH 2,6-DIAMINO-8-(1H-IMIDAZOL-2-YLSULFANYLMETHYL)-3H-QUINAZOLINE-4-ONE | ||||||
![]() | TRNA-GUANINE TRANSGLYCOSYLASE | ||||||
![]() | TRANSFERASE / TRNA-MODIFYING ENZYME / GLYCOSYLTRANSFERASE | ||||||
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 | ![]() ![]() | ||||||
![]() | Brenk, R. / Meyer, E.A. / Castellano, R.K. / Furler, M. / Stubbs, M.T. / Klebe, G. / Diederich, F. | ||||||
![]() | ![]() Title: De novo design, synthesis, and in vitro evaluation of inhibitors for prokaryotic tRNA-guanine transglycosylase: a dramatic sulfur effect on binding affinity. Authors: Meyer, E.A. / Brenk, R. / Castellano, R.K. / Furler, M. / Klebe, G. / Diederich, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 95.6 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 735.5 KB | Display | ![]() |
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Full document | ![]() | 741.5 KB | Display | |
Data in XML | ![]() | 19.7 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1k4hC ![]() 1pudS 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
#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-AIQ / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.64 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: TRIS, PEG 8000, DMSO, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 290K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 Details: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 28, 2001 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→100 Å / Num. obs: 44700 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Rsym value: 0.053 / Net I/σ(I): 14.49 |
Reflection shell | Resolution: 1.7→1.76 Å / Mean I/σ(I) obs: 3.85 / Rsym value: 0.29 / % possible all: 99.2 |
Reflection | *PLUS Num. measured all: 406718 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PUD Resolution: 1.7→40.8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.7→40.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.73 Å
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Refinement | *PLUS Num. reflection obs: 44700 / Rfactor obs: 0.199 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.367 |