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- PDB-5ccx: Structure of the product complex of tRNA m1A58 methyltransferase ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ccx | ||||||||||||
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Title | Structure of the product complex of tRNA m1A58 methyltransferase with tRNA3Lys as substrate | ||||||||||||
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![]() | TRANSFERASE/RNA / tRNA modification / Sam-dependent methyltransferase class I / methyltransferase fold / HIV-1 primer / TRANSFERASE-RNA complex | ||||||||||||
Function / homology | ![]() mRNA (adenine-N1-)-methyltransferase activity / tRNA (adenine(58)-N1)-methyltransferase activity / tRNA (adenine58-N1)-methyltransferase / tRNA (m1A) methyltransferase complex / tRNA modification in the nucleus and cytosol / : / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / RNA binding / nucleoplasm / nucleus Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Finer-Moore, J. / Czudnochowski, N. / O'Connell III, J.D. / Wang, A.L. / Stroud, R.M. | ||||||||||||
Funding support | ![]() ![]()
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![]() | ![]() Title: Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target. Authors: Finer-Moore, J. / Czudnochowski, N. / O'Connell, J.D. / Wang, A.L. / Stroud, R.M. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 310.7 KB | Display | ![]() |
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PDB format | ![]() | 246.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 812.4 KB | Display | ![]() |
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Full document | ![]() | 828.7 KB | Display | |
Data in XML | ![]() | 31.4 KB | Display | |
Data in CIF | ![]() | 45.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5ccbSC ![]() 5cd1C 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
-TRNA (adenine(58)-N(1))-methyltransferase ... , 2 types, 2 molecules AB
#1: Protein | Mass: 31420.627 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): modified to contain a 3C protease cleavage site C-terminal to the 6His-tag Cell line (production host): BL21(DE3) / Production host: ![]() ![]() References: UniProt: Q96FX7, tRNA (adenine58-N1)-methyltransferase |
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#2: Protein | Mass: 55883.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): modified to contain a 3C protease cleavage site C-terminal to the 6His tag Cell line (production host): BL21(DE3) / Production host: ![]() ![]() |
-RNA chain , 1 types, 1 molecules N
#3: RNA chain | Mass: 24806.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 3 types, 311 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-SAH / |
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#5: Chemical | ChemComp-NA / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.69 Å3/Da / Density % sol: 66.71 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAM, 1mM MgCl2 and 50mM Hepes pH 7.5) plus 1 microliter reservoir solution (0.1 M NaAcetate, pH 4.8-5.0, 2% ...Details: 1 microliter protein solution (4.8 mg/ml protein, 66.4 micromolar tRNA3Lys, 2mM SAM, 1mM MgCl2 and 50mM Hepes pH 7.5) plus 1 microliter reservoir solution (0.1 M NaAcetate, pH 4.8-5.0, 2% w/v PEG 4000 and 15% v/v MPD) over 1000 microliters reservoir solution PH range: 4.8-5.0 |
-Data collection
Diffraction | Mean temperature: 103 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2014 |
Radiation | Monochromator: double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→108 Å / Num. obs: 98180 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 16.7 |
Reflection shell | Resolution: 2.1→2.15 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.59 / Mean I/σ(I) obs: 0.9 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5CCB Resolution: 2.1→54.13 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.25 / 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: 2.1→54.13 Å
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Refine LS restraints |
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LS refinement shell |
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