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Yorodumi- PDB-4q4q: tRNA-Guanine Transglycosylase (TGT) in Complex with 2-[(Thiophen-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4q4q | |||||||||
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Title | tRNA-Guanine Transglycosylase (TGT) in Complex with 2-[(Thiophen-2-ylmethyl)amino]-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one | |||||||||
Components | Queuine tRNA-ribosyltransferase | |||||||||
Keywords | Transferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / preQ1 / tRNA / Transferase-transferase inhibitor complex | |||||||||
Function / homology | Function and homology information 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 | Zymomonas mobilis subsp. mobilis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å | |||||||||
Authors | Neeb, M. / Heine, A. / Klebe, G. | |||||||||
Citation | Journal: J.Med.Chem. / Year: 2014 Title: Beyond Affinity: Enthalpy-Entropy Factorization Unravels Complexity of a Flat Structure-Activity Relationship for Inhibition of a tRNA-Modifying Enzyme. Authors: Neeb, M. / Betz, M. / Heine, A. / Barandun, L.J. / Hohn, C. / Diederich, F. / Klebe, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q4q.cif.gz | 177.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q4q.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 4q4q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q4/4q4q ftp://data.pdbj.org/pub/pdb/validation_reports/q4/4q4q | HTTPS FTP |
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-Related structure data
Related structure data | 4q4oC 4q4pC 4q4rC 4q4sC 1pudS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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 / Fragment: Guanine Insertion Enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) Zymomonas mobilis subsp. mobilis (bacteria) Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pET9d-ZM4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase | ||||||
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#2: Chemical | ChemComp-ZN / | ||||||
#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-SAQ / | #5: Water | ChemComp-HOH / | Sequence details | AUTHORS HAVE INDICATED THE CORRECT RESIDUE AT THE POSITION IS LYS. E.G. REUTER K. K. H., FICNER R.; ...AUTHORS HAVE INDICATED THE CORRECT RESIDUE AT THE POSITION IS LYS. E.G. REUTER K. K. H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995). | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.05 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 14, 2010 / 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: 1.41→30 Å / Num. obs: 78370 / % possible obs: 99.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 10.7 Å2 / Rsym value: 0.071 / Net I/σ(I): 15.6 |
Reflection shell | Resolution: 1.41→1.43 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 3931 / Rsym value: 0.491 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 1PUD Resolution: 1.41→25.206 Å / SU ML: 0.11 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 14.89 / 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: 1.41→25.206 Å
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Refine LS restraints |
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LS refinement shell |
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