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Yorodumi- PDB-5eov: C-terminal domain of the 16S/23S rRNA (cytidine-2'-O)-methyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5eov | ||||||
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Title | C-terminal domain of the 16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA. | ||||||
Components | 16S/23S rRNA (cytidine-2'-O)-methyltransferase TlyA | ||||||
Keywords | TRANSFERASE / methyltransferase / ribosome / antibiotic sensitivity | ||||||
Function / homology | Function and homology information 16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / hemolysis in another organism / cell wall / : / methyltransferase activity / rRNA processing / toxin activity / methylation / host cell plasma membrane ...16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / hemolysis in another organism / cell wall / : / methyltransferase activity / rRNA processing / toxin activity / methylation / host cell plasma membrane / RNA binding / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å | ||||||
Authors | Witek, M.A. / Conn, G.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: J. Biol. Chem. / Year: 2017 Title: A Novel Motif for S-Adenosyl-l-methionine Binding by the Ribosomal RNA Methyltransferase TlyA from Mycobacterium tuberculosis. Authors: Witek, M.A. / Kuiper, E.G. / Minten, E. / Crispell, E.K. / Conn, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5eov.cif.gz | 92.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5eov.ent.gz | 68.4 KB | Display | PDB format |
PDBx/mmJSON format | 5eov.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/5eov ftp://data.pdbj.org/pub/pdb/validation_reports/eo/5eov | HTTPS FTP |
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-Related structure data
Related structure data | 5ks2C 5kygC 3hp7S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 23089.346 Da / Num. of mol.: 1 / Fragment: residues 64-268 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: CDC 1551 / Oshkosh / Gene: tlyA, MT1733 / Production host: Escherichia coli (E. coli) References: UniProt: P9WJ62, 23S rRNA (cytidine1920-2'-O)-methyltransferase, 16S rRNA (cytidine1409-2'-O)-methyltransferase |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.49 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.3 M Hepes pH 7.5, 2.8 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Apr 14, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 21238 / % possible obs: 100 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 65.2 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 3.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Homology model based on 3HP7 Resolution: 1.701→47.93 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.52 / 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: 1.701→47.93 Å
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Refine LS restraints |
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LS refinement shell |
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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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