+Open data
-Basic information
Entry | Database: PDB / ID: 5kyg | ||||||
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Title | RAWV_CTD (Loop Structure) of 16S/23S 2'-O-methyltransferase TlyA | ||||||
Components | Cytotoxin / haemolysin homologue TlyA | ||||||
Keywords | TRANSFERASE / Methyltransferase / Hemolysin / ribosome / antibiotic sensitivity | ||||||
Function / homology | Function and homology information 16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / hemolysis by symbiont of host erythrocytes / rRNA methyltransferase activity / rRNA methylation / methyltransferase activity / methylation / toxin activity / killing of cells of another organism / host cell plasma membrane ...16S rRNA (cytidine1409-2'-O)-methyltransferase / 23S rRNA (cytidine1920-2'-O)-methyltransferase / hemolysis by symbiont of host erythrocytes / rRNA methyltransferase activity / rRNA methylation / methyltransferase activity / methylation / toxin activity / killing of cells of another organism / 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: 1.9 Å | ||||||
Authors | Kuiper, E.G. / Conn, G.L. | ||||||
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 | 5kyg.cif.gz | 92.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5kyg.ent.gz | 69.4 KB | Display | PDB format |
PDBx/mmJSON format | 5kyg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ky/5kyg ftp://data.pdbj.org/pub/pdb/validation_reports/ky/5kyg | HTTPS FTP |
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-Related structure data
Related structure data | 5eovSC 5ks2C 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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Details | Monomer as determined by Gel-filtration. |
-Components
#1: Protein | Mass: 23690.039 Da / Num. of mol.: 1 / Fragment: residues 15-223 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: tlyA, ERS007722_00402 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0U0QZA7, UniProt: P9WJ63*PLUS, 23S rRNA (cytidine1920-2'-O)-methyltransferase |
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#2: Chemical | ChemComp-GOL / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 42.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 8% Tascimate pH 8.0, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 80 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 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→53.04 Å / Num. obs: 16678 / % possible obs: 99.87 % / Redundancy: 12.8 % / CC1/2: 0.928 / Rmerge(I) obs: 0.121 / Net I/σ(I): 45.8 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 3.6 / CC1/2: 0.928 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5EOV Resolution: 1.9→53.04 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.28 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.143 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.628 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→53.04 Å
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