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- PDB-7a6d: tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in c... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7a6d | ||||||
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Title | tRNA-guanine transglycosylase C158S/C281S/Y330C/H333A mutant in complex with rac-trans-4,4-difluorocyclopentane-1,2-diol | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / enzyme / disulfide / fragment | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Nguyen, D. / Heine, A. / Klebe, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Targeting a Cryptic Pocket in a Protein-Protein Contact by Disulfide-Induced Rupture of a Homodimeric Interface. Authors: Nguyen, D. / Xie, X. / Jakobi, S. / Terwesten, F. / Metz, A. / Nguyen, T.X.P. / Palchykov, V.A. / Heine, A. / Reuter, K. / 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 | ![]() | 279.4 KB | Display | ![]() |
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PDB format | ![]() | 189.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4jbrC ![]() 7a0bC ![]() 7a3vC ![]() 7a3xC ![]() 7a4kC ![]() 7a4xC ![]() 7a9eC ![]() 7adnC ![]() 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42910.605 Da / Num. of mol.: 1 / Mutation: C158S/C281S/Y330C/H333A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pPR-IBA2 / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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-Non-polymers , 6 types, 269 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/R1E.gif)
![](data/chem/img/RGN.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/R1E.gif)
![](data/chem/img/RGN.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-R1E / | #6: Chemical | ChemComp-RGN / ( | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.17 Å3/Da / Density % sol: 61.17 % / Description: hexagonal bipyramidal |
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Crystal grow | Temperature: 283.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M TRIS, pH 8.5, 4% PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→42.79 Å / Num. obs: 74885 / % possible obs: 99.8 % / Redundancy: 17.5 % / Biso Wilson estimate: 25.05 Å2 / CC1/2: 1 / Rsym value: 0.08 / Net I/σ(I): 21.7 |
Reflection shell | Resolution: 1.59→1.68 Å / Redundancy: 17.9 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 11815 / CC1/2: 0.609 / Rsym value: 2.058 / % possible all: 99.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PUD Resolution: 1.59→42.79 Å / SU ML: 0.1447 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.3237 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.09 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→42.79 Å
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Refine LS restraints |
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LS refinement shell |
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