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- PDB-5hji: Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hji | ||||||||||||
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Title | Crystal Structure of Pyrococcus abyssi Trm5a complexed with adenosine | ||||||||||||
![]() | tRNA (guanine(37)-N1)-methyltransferase Trm5a | ||||||||||||
![]() | TRANSFERASE / Methyltransferase / Trm5a / SAM / Adenosine / tRNA modification | ||||||||||||
Function / homology | ![]() tRNA N1-guanine methylation / tRNA (guanine37-N1)-methyltransferase / tRNA (guanine(37)-N1)-methyltransferase activity / tRNA methylation / Transferases; Transferring one-carbon groups; Methyltransferases / cytoplasm Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() | ||||||||||||
![]() | Xie, W. / Wang, C. / Jia, Q. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structures of the bifunctional tRNA methyltransferase Trm5a Authors: Wang, C. / Jia, Q. / Chen, R. / Wei, Y. / Li, J. / Ma, J. / Xie, W. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91.9 KB | Display | ![]() |
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PDB format | ![]() | 66.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 760.6 KB | Display | ![]() |
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Full document | ![]() | 762 KB | Display | |
Data in XML | ![]() | 16.7 KB | Display | |
Data in CIF | ![]() | 24.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5hjjC ![]() 5hjkSC ![]() 5hjmC 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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Unit cell |
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Components
#1: Protein | Mass: 40758.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: GE5 / Orsay / Gene: trm5a, PYRAB01130, PAB2272 / Plasmid: pET-28a(+) / Production host: ![]() ![]() References: UniProt: Q9V2G1, tRNA (guanine37-N1)-methyltransferase |
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#2: Chemical | ChemComp-ADN / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 10-15% PEG3350, 100mM HEPES, pH7.5, 100mM Ca(OAc)2 and 100mM KCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: OXFORD ONYX CCD / Detector: CCD / Date: Nov 5, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→24.574 Å / Num. obs: 19382 / % possible obs: 99.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 8 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.3 / % possible all: 98.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5HJK Resolution: 2.2→24.574 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.72
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→24.574 Å
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Refine LS restraints |
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LS refinement shell |
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