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- PDB-3c2y: tRNA-Guanine Transglycosylase (TGT) in complex with 6-Amino-2-met... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3c2y | ||||||
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Title | tRNA-Guanine Transglycosylase (TGT) in complex with 6-Amino-2-methyl-1,7-dihydro-imidazo[4,5-g]quinazolin-8-one | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / TIM Barrel / Glycosyltransferase / Metal-binding / Queuosine biosynthesis / tRNA processing | ||||||
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 | ![]() ![]() | ||||||
![]() | Ritschel, T. / Heine, A. / Klebe, G. | ||||||
![]() | ![]() Title: Crystal structure analysis and in silico pKa calculations suggest strong pKa shifts of ligands as driving force for high-affinity binding to TGT Authors: Ritschel, T. / Hoertner, S. / 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 | ![]() | 93.2 KB | Display | ![]() |
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PDB format | ![]() | 67.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2z7kC ![]() 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 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-S60 / | ||||
#4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Sequence details | THERE IS A MISTAKE IN SWISSPROT FOR P28720. THIS IS REFERRED IN THE ORIGINAL PAPER; REUTER K.K.H., ...THERE IS A MISTAKE IN SWISSPROT FOR P28720. THIS IS REFERRED IN THE ORIGINAL PAPER; REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995). THE CORRECT RESIDUE AT THE POSITION IS LYS. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.1 % |
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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: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 12, 2006 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→50 Å / Num. all: 36907 / Num. obs: 36907 / % possible obs: 95 % / Redundancy: 1.9 % / Rsym value: 0.055 / Net I/σ(I): 15 |
Reflection shell | Resolution: 1.78→1.81 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 1780 / Rsym value: 0.37 / % possible all: 92.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1P0D Resolution: 1.78→10 Å / Num. parameters: 12544 / Num. restraintsaints: 11778 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & 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: 2724 / Occupancy sum non hydrogen: 3109.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.78→10 Å
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Refine LS restraints |
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