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- PDB-1p0b: Crystal Structure Of tRNA-Guanine Transglycosylase (TGT) From Zym... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1p0b | ||||||
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Title | Crystal Structure Of tRNA-Guanine Transglycosylase (TGT) From Zymomonas mobilis Complexed With Archaeosine Precursor, Preq0 | ||||||
![]() | Queuine tRNA-ribosyltransferase | ||||||
![]() | TRANSFERASE / substrate-protein-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 | ![]() ![]() | ||||||
![]() | Brenk, R. / Stubbs, M.T. / Heine, A. / Reuter, K. / Klebe, G. | ||||||
![]() | ![]() Title: Flexible adaptations in the structure of the tRNA-modifying enzyme tRNA-guanine transglycosylase and their implications for substrate selectivity, reaction mechanism and structure-based drug design Authors: Brenk, R. / Stubbs, M.T. / Heine, A. / Reuter, K. / 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 | ![]() | 95.7 KB | Display | ![]() |
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PDB format | ![]() | 70.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 450.1 KB | Display | ![]() |
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Full document | ![]() | 456.8 KB | Display | |
Data in XML | ![]() | 19.9 KB | Display | |
Data in CIF | ![]() | 30.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ozmC ![]() 1ozqC ![]() 1p0dC ![]() 1p0eC ![]() 1pudS S: Starting model for refinement 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
#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-PQ0 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.45 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: PEG 8000, MES, DMSO, DTT, preQ0, pH 5.50, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / pH: 7.5 / Method: vapor diffusion, hanging dropDetails: Romier, C., (1996) Proteins: Struct.,Funct., Genet., 24, 516. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 6, 2003 / Details: MIRRORS |
Radiation | Monochromator: YALE MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. all: 43081 / Num. obs: 43081 / % possible obs: 95.6 % / Redundancy: 3.8 % / Biso Wilson estimate: 22.1 Å2 / Rsym value: 0.104 |
Reflection shell | Resolution: 1.7→1.73 Å / Rsym value: 0.562 / % possible all: 92.2 |
Reflection | *PLUS Num. measured all: 163734 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS % possible obs: 92.2 % / Rmerge(I) obs: 0.562 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PUD Resolution: 1.7→20 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 502883.26 / Data cutoff high rms absF: 502883.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0799 Å2 / ksol: 0.31791 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.2 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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