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- PDB-4puj: tRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-{[2... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4puj | |||||||||
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Title | tRNA-Guanine Transglycosylase (TGT) in Complex with 6-Amino-2-{[2-(morpholin-4-yl)ethyl]amino}-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one | |||||||||
![]() | Queuine tRNA-ribosyltransferase | |||||||||
![]() | transferase/transferase inhibitor / Transferase / Guanine Exchange Enzyme / Guanine / preQ1 / 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 | ![]() ![]() ![]() | |||||||||
![]() | Neeb, M. / Heine, A. / Klebe, G. | |||||||||
![]() | ![]() Title: Chasing Protons: How Isothermal Titration Calorimetry, Mutagenesis, and pKa Calculations Trace the Locus of Charge in Ligand Binding to a tRNA-Binding Enzyme. Authors: Neeb, M. / Czodrowski, P. / Heine, A. / Barandun, L.J. / Hohn, C. / 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 | ![]() | 177.4 KB | Display | ![]() |
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PDB format | ![]() | 138.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 453.1 KB | Display | ![]() |
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Full document | ![]() | 454.5 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 27.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4pukC ![]() 4pulC ![]() 4pumC ![]() 4punC ![]() 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: 42925.703 Da / Num. of mol.: 1 / Fragment: Guanine Insertion Enzyme Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 31821 / ZM4 / CP4 / Gene: tgt, ZMO0363 / Plasmid: pET9d-ZM4 / Production host: ![]() ![]() References: UniProt: P28720, tRNA-guanosine34 preQ1 transglycosylase |
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-Non-polymers , 5 types, 395 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CKR.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/CKR.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ZN / | ||||||
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#3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-CL / | #5: Chemical | ChemComp-CKR / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | AUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. ...AUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE AT THE POSITION IS LYS (REUTER K.K.H., FICNER R.; J. BACTERIOL. 177:5284-5288(1995)) |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.07 % |
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Crystal grow | Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100 mM MES, 10% DMSO, 13% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2012 / 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: 1.42→30 Å / Num. obs: 76897 / % possible obs: 99.3 % / Redundancy: 5.2 % / Biso Wilson estimate: 12.8 Å2 / Rsym value: 0.057 / Net I/σ(I): 28.6 |
Reflection shell | Resolution: 1.42→1.44 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 3785 / Rsym value: 0.505 / % possible all: 98.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PUD Resolution: 1.42→27.24 Å / SU ML: 0.11 / Cross valid method: R-free / σ(F): 1.35 / Phase error: 14.76 / 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: 1.42→27.24 Å
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Refine LS restraints |
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LS refinement shell |
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