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- PDB-4gkt: tRNA Guanine Transglycosylase in complex with disubstituted lin-b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4gkt | ||||||
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Title | tRNA Guanine Transglycosylase in complex with disubstituted lin-benzoguanine inhibitor | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TIM BARREL / GLYCOSYLTRANSFERASE / QUEUOSINE / BIOSYNTHESIS / TRNA PROCESSING / 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 | ![]() ![]() | ||||||
![]() | Immekus, F. / Klebe, G. | ||||||
![]() | ![]() Title: Two-armed benzopurine inhibitors of TGT Authors: Immekus, F. / Barandun, L.J. / 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 | ![]() | 89.8 KB | Display | ![]() |
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PDB format | ![]() | 64.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.5 KB | Display | ![]() |
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Full document | ![]() | 732.4 KB | Display | |
Data in XML | ![]() | 17.3 KB | Display | |
Data in CIF | ![]() | 25.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4gg9C ![]() 4gh1C ![]() 4gh3C ![]() 4gi4C ![]() 4giyC ![]() 1p0dS 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: 42925.703 Da / Num. of mol.: 1 / Mutation: T312K Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: PET9D / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-0O1 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 48.75 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100MM MES, 1MM DTT, 10% DMSO, 13% PEG8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Mar 15, 2012 / Details: Rh coated silicon with indirect water cooling |
Radiation | Monochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→50 Å / Num. all: 61168 / Num. obs: 61168 / % possible obs: 99.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.059 / Net I/σ(I): 18.03 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.65 / Num. unique all: 3062 / Rsym value: 0.386 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: AB INITIO Starting model: 1P0D Resolution: 1.53→50 Å / Num. parameters: 11839 / Num. restraintsaints: 11182 / 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: 4 / Occupancy sum hydrogen: 2591.97 / Occupancy sum non hydrogen: 2943.47 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.53→50 Å
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Refine LS restraints |
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