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Yorodumi- PDB-3fuw: T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fuw | ||||||
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Title | T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with 5'-methylthioadenosine in space group P212121 | ||||||
Components | Dimethyladenosine transferase | ||||||
Keywords | TRANSFERASE / Methyltransferase / dimethyltransferase / dual-specific methyltransferase / 16S rRNA methyltransferase / translation / Antibiotic resistance / RNA-binding / rRNA processing / S-adenosyl-L-methionine | ||||||
Function / homology | Function and homology information 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase / 16S rRNA (adenine(1518)-N(6)/adenine(1519)-N(6))-dimethyltransferase activity / RNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.56 Å | ||||||
Authors | Demirci, H. / Belardinelli, R. / Seri, E. / Gregory, S.T. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2009 Title: Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. Authors: Demirci, H. / Belardinelli, R. / Seri, E. / Gregory, S.T. / Gualerzi, C. / Dahlberg, A.E. / Jogl, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fuw.cif.gz | 74.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fuw.ent.gz | 54 KB | Display | PDB format |
PDBx/mmJSON format | 3fuw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fuw ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fuw | HTTPS FTP |
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-Related 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: 29908.951 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: cytoplasm / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: ksgA, TTHA0083 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)Star References: UniProt: Q5SM60, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Chemical | ChemComp-MTA / |
#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: 2.25 Å3/Da / Density % sol: 45.32 % |
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Crystal grow | Temperature: 277 K / Method: microbatch technique under oil / pH: 8.5 Details: 17% w/v polyethylene glycol 4000, 85 mM HEPES-NaOH (pH 8.5), 8.5% v/v isopropanol and 15% v/v anhydrous glycerol, microbatch technique under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9797 Å |
Detector | Type: MAR CCD 130 mm / Detector: CCD Details: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror |
Radiation | Monochromator: Bent single Si (111) crystal monochromator (horizontal focusing and deflection) with vertical focusing mirror Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→30 Å / Num. obs: 38372 / % possible obs: 97 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 26.67 |
Reflection shell | Resolution: 1.56→1.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.64 / Num. unique all: 3682 / % possible all: 94.5 |
-Processing
Software |
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Refinement | Resolution: 1.56→28.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.08 / SU B: 3.348 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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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 max: 75.79 Å2 / Biso mean: 19.766 Å2 / Biso min: 4.55 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→28.63 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.56→1.6 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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