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- PDB-3v97: Crystal structure of bifunctional methyltransferase YcbY (RlmLK) ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3v97 | |||||||||
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Title | Crystal structure of bifunctional methyltransferase YcbY (RlmLK) from Escherichia coli, SAH binding | |||||||||
![]() | Ribosomal RNA large subunit methyltransferase L | |||||||||
![]() | TRANSFERASE / YcbY / RNA methyltransferase / ribosome RNA / SAH / RlmKL / RlmL | |||||||||
Function / homology | ![]() 23S rRNA (guanine2445-N2)-methyltransferase / 23S rRNA (guanine2069-N7)-methyltransferase / 23S rRNA (guanine(2445)-N(2))-methyltransferase activity / rRNA (guanine-N2-)-methyltransferase activity / rRNA (guanine-N7-)-methyltransferase activity / rRNA base methylation / rRNA methylation / RNA binding / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Su, X.D. / Wang, K.T. | |||||||||
![]() | ![]() Title: Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA Authors: Wang, K.T. / Desmolaize, B. / Nan, J. / Zhang, X.W. / Li, L.F. / Douthwaite, S. / Su, X.D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 525.4 KB | Display | ![]() |
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PDB format | ![]() | 429.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 56.8 KB | Display | |
Data in CIF | ![]() | 79.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3v8vC ![]() 2b78S ![]() 3ldfS ![]() 3ldgS 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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 79032.078 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P75864, 23S rRNA (guanine2445-N2)-methyltransferase #2: Polysaccharide | #3: Chemical | ChemComp-SAH / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.7 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M HEPES, 12%(w/v) PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 1, 2010 |
Radiation | Monochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 99787 / % possible obs: 96.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 |
Reflection shell | Highest resolution: 2.2 Å / % possible all: 96.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2B78, 3LDG, 3LDF Resolution: 2.2→49.91 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.934 / SU B: 12.381 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.91 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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