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Yorodumi- PDB-3fuu: T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fuu | ||||||
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Title | T. thermophilus 16S rRNA A1518 and A1519 methyltransferase (KsgA) in complex with Adenosine 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: 1.53 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 | 3fuu.cif.gz | 75.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fuu.ent.gz | 55.1 KB | Display | PDB format |
PDBx/mmJSON format | 3fuu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/3fuu ftp://data.pdbj.org/pub/pdb/validation_reports/fu/3fuu | 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 | #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: 45.41 % |
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Crystal grow | Temperature: 277 K / Method: microbatch technique under oil / pH: 7.5 Details: 50 mM magnesium chloride hexahydrate, 100 mM HEPES (pH 7.5) and 30% v/v polyethylene glycol monomethyl ether 550, 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: 1.53→25 Å / Num. obs: 41095 / % possible obs: 98.3 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.27 |
Reflection shell | Resolution: 1.53→1.57 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.2 / Num. unique all: 4080 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Resolution: 1.53→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0 / SU B: 3.127 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.103 / 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 max: 63.07 Å2 / Biso mean: 25.428 Å2 / Biso min: 14.93 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 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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