+Open data
-Basic information
Entry | Database: PDB / ID: 5co4 | ||||||
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Title | Structural insights into the 2-OH methylation of C/U34 on tRNA | ||||||
Components | Putative tRNA (cytidine(34)-2'-O)-methyltransferase | ||||||
Keywords | TRANSFERASE / TrmL / methyltrnasferase / S-adenosyl-L-methionine / methylthioadensine / catalytic mechanism | ||||||
Function / homology | Function and homology information tRNA (cytidine34-2'-O)-methyltransferase / tRNA methyltransferase activity / S-adenosylmethionine-dependent methyltransferase activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus HB27 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Xie, W. / Pang, P. / Wang, Z. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: Structural insights into the 2-OH methylation of C34 or U34 on tRNA Authors: Xie, W. / Pang, P. / Wang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5co4.cif.gz | 85.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5co4.ent.gz | 61.7 KB | Display | PDB format |
PDBx/mmJSON format | 5co4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/co/5co4 ftp://data.pdbj.org/pub/pdb/validation_reports/co/5co4 | HTTPS FTP |
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-Related structure data
Related structure data | 4jakS S: Starting model for refinement |
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Similar structure data |
-Links
-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: 20055.209 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Strain: HB27 / Gene: TT_C1952 / Production host: Escherichia coli Bl21(DE3) (bacteria) / Strain (production host): Bl21(DE3) References: UniProt: Q72G96, tRNA (cytidine34-2'-O)-methyltransferase #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.02 Å3/Da / Density % sol: 39.1 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 16% PEG 3350, 0.6 M NaCl, 0.1 M MES (pH 6.5) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 35125 / % possible obs: 100 % / Redundancy: 11.1 % / Net I/σ(I): 38.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 5.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4jak Resolution: 1.7→37.689 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.25 / 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: 1.7→37.689 Å
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Refine LS restraints |
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LS refinement shell |
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