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- PDB-3sm0: tRNA-Guanine Transglycosylase in complex with lin-Benzohypoxanthi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3sm0 | ||||||
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Title | tRNA-Guanine Transglycosylase in complex with lin-Benzohypoxanthine Inhibitor | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE/TRANSFERASE INHIBITOR / TIM BARREL / GLYCOSYLTRANSFERASE / METAL-BINDING / QUEUOSINE / BIOSYNTHESIS / TRANSFERASE / 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 | ![]() ![]() | ||||||
![]() | Klebe, G. / Immekus, F. / Heine, A. | ||||||
![]() | ![]() Title: From lin-Benzoguanines to lin-Benzohypoxanthines as Ligands for Zymomonas mobilis tRNA-Guanine Transglycosylase: Replacement of Protein-Ligand Hydrogen Bonding by Importing Water Clusters. Authors: Barandun, L.J. / Immekus, F. / Kohler, P.C. / Tonazzi, S. / Wagner, B. / Wendelspiess, S. / Ritschel, T. / Heine, A. / Kansy, 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 | ![]() | 91.7 KB | Display | ![]() |
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PDB format | ![]() | 66.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 736.8 KB | Display | ![]() |
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Full document | ![]() | 741.9 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3rr4C ![]() 3s1gC ![]() 3tllC ![]() 3gfn 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 on special symmetry positions |
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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-AEK / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 49.48 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 100MM TRIS HCL, 1MM DTT, 10% DMSO, 5% PEG 8000 , 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: Dec 10, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.57→25 Å / Num. all: 54458 / Num. obs: 54458 / % possible obs: 93.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 16.42 Å2 / Rsym value: 0.056 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.57→1.6 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.74 / Rsym value: 0.27 / % possible all: 83.9 |
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Processing
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Refinement | Method to determine structure: AB INITIO / Resolution: 1.57→25 Å / Num. parameters: 12381 / Num. restraintsaints: 11634 / 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: 6 / Occupancy sum hydrogen: 2662 / Occupancy sum non hydrogen: 3058.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.57→25 Å
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Refine LS restraints |
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