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- PDB-3ftc: Crystal structure of A. aeolicus KsgA at 1.72-Angstrom resolution -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ftc | ||||||
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Title | Crystal structure of A. aeolicus KsgA at 1.72-Angstrom resolution | ||||||
![]() | Dimethyladenosine transferase | ||||||
![]() | TRANSFERASE / KsgA / Rossmann-like fold / RNA Methyltransferase / MTase / Antibiotic resistance / Methyltransferase / RNA-binding / rRNA processing / S-adenosyl-L-methionine | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Tu, C. / Ji, X. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.3 KB | Display | ![]() |
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PDB format | ![]() | 46.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3ftdC ![]() 3fteC ![]() 3ftfC ![]() 1qyrS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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. |
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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.) ![]() ![]() ![]() ![]() References: UniProt: O67680, Transferases; Transferring one-carbon groups; Methyltransferases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.61 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 25% PEG 3000, 0.1 M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
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: 1.68→30 Å / Num. all: 25134 / Num. obs: 25134 / % possible obs: 92.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 25.7 |
Reflection shell | Resolution: 1.68→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.7 / Num. unique all: 1466 / % possible all: 54.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1QYR Resolution: 1.68→28.51 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber Details: 1. THE EFFECTIVE RESOLUTION FOR THIS STRUCTURE IS 1.72 ANGSTROM, AT WHICH THE COMPLETENESS OF X-RAY DATA > 93% AND THE OBSERVABLE DATA > 70% FOR HIGHEST RESOLUTION SHELL. 2. HYDROGENS HAVE ...Details: 1. THE EFFECTIVE RESOLUTION FOR THIS STRUCTURE IS 1.72 ANGSTROM, AT WHICH THE COMPLETENESS OF X-RAY DATA > 93% AND THE OBSERVABLE DATA > 70% FOR HIGHEST RESOLUTION SHELL. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Displacement parameters | Biso mean: 31.282 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→28.51 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: 6
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