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- PDB-4q8v: tRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4q8v | ||||||
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Title | tRNA-Guanine Transglycosylase (TGT) in Complex with 4-[2-({6-Amino-8-oxo-1H,7H,8H-imidazo[4,5-g]quinazolin-2-yl}amino)ethyl]benzonitrile | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | Transferase/transferase inhibitor / Guanine Exchange Enzyme / preQ1 / tRNA / Transferase-transferase inhibitor complex | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Neeb, M. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Addressing a New Subpocket of TGT by Elongated 2-Amino-lin-benzoguanines Authors: Neeb, M. / Hohn, C. / Heine, A. / Diederich, F. / Klebe, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 175.3 KB | Display | ![]() |
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PDB format | ![]() | 137 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 634.1 KB | Display | ![]() |
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Full document | ![]() | 634.7 KB | Display | |
Data in XML | ![]() | 18.4 KB | Display | |
Data in CIF | ![]() | 28.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4q8tC ![]() 4q8uC ![]() 4q8wC ![]() 1pudS C: citing same article ( S: Starting model for refinement |
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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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Components
#1: Protein | Mass: 43069.828 Da / Num. of mol.: 1 / Fragment: Guanine Insertion Enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2-ZM-WT / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-2YX / |
#5: Water | ChemComp-HOH / |
Sequence details | AUTHORS HAVE INDICATED THAT THERE IS A CONFLICT IN THE UNPROT SEQUENCE P28720. SEE REFERENCE: ...AUTHORS HAVE INDICATED THAT THERE IS A CONFLICT IN THE UNPROT SEQUENCE P28720. SEE REFERENCE: REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288 (1995). THE CORRECT RESIDUE IS A LYS |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.23 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 13, 2013 / Details: Mirror |
Radiation | Monochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→50 Å / Num. obs: 79794 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Biso Wilson estimate: 12.1 Å2 / Rsym value: 0.062 / Net I/σ(I): 11 |
Reflection shell | Resolution: 1.4→1.48 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Num. unique all: 12619 / Rsym value: 0.483 / % possible all: 95.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1PUD Resolution: 1.396→21.823 Å / SU ML: 0.14 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 15.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.396→21.823 Å
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Refine LS restraints |
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LS refinement shell |
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