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Yorodumi- PDB-3ftd: Crystal structure of A. aeolicus KsgA at 1.44-Angstrom resolution -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ftd | ||||||
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Title | Crystal structure of A. aeolicus KsgA at 1.44-Angstrom resolution | ||||||
Components | Dimethyladenosine transferase | ||||||
Keywords | TRANSFERASE / KsgA / Rossmann-like fold / RNA Methyltransferase / MTase / Antibiotic resistance / Methyltransferase / 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 / rRNA (adenine-N6,N6-)-dimethyltransferase activity / rRNA methylation / RNA binding / cytosol Similarity search - Function | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å | ||||||
Authors | Tu, C. / Ji, X. | ||||||
Citation | Journal: Structure / Year: 2009 Title: Structural Basis for Binding of RNA and Cofactor by a KsgA Methyltransferase. Authors: Tu, C. / Tropea, J.E. / Austin, B.P. / Court, D.L. / Waugh, D.S. / Ji, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ftd.cif.gz | 120.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ftd.ent.gz | 93.4 KB | Display | PDB format |
PDBx/mmJSON format | 3ftd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/3ftd ftp://data.pdbj.org/pub/pdb/validation_reports/ft/3ftd | HTTPS FTP |
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-Related structure data
Related structure data | 3ftcSC 3fteC 3ftfC 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 | The biological assembly corresponds to the content of the asymmetric unit. |
-Components
#1: Protein | Mass: 28484.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: genomic DNA / Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: aq_1816, ksgA / Plasmid: pBA1939 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: O67680, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: 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: 1.9 Å3/Da / Density % sol: 35.31 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 20% PEG MME 5000, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 13, 2008 / Details: mirrors |
Radiation | Monochromator: Si(111) Rosenbaum-Rock double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.44→30 Å / Num. all: 38594 / Num. obs: 38594 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 24.6 |
Reflection shell | Resolution: 1.44→1.48 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 1.9 / Num. unique all: 3121 / Rsym value: 0.493 / % possible all: 66 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3FTC Resolution: 1.44→28.691 Å / SU ML: 0.17 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.043 Å2 / ksol: 0.375 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.44→28.691 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14
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