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- PDB-2ih5: Crystal structure of the adenine-specific DNA methyltransferase M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ih5 | ||||||
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Title | Crystal structure of the adenine-specific DNA methyltransferase M.TaqI complexed with the cofactor analog AETA and a 10 bp DNA containing an abasic site analog at the target base partner position | ||||||
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![]() | TRANSFERASE/DNA / DNA / DNA methyltransferase / target base partner / abasic site analog / base flipping / nucleotide flipping / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA restriction-modification system / methylation / DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lenz, T. / Scheidig, A.J. / Weinhold, E. | ||||||
![]() | ![]() Title: Influence of the target base partner on the methylation rate of the adenine-specific DNA methyltransferase M.TaqI Authors: Lenz, T. / Scheidig, A.J. / Weinhold, E. #1: ![]() Title: Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog Authors: Goedecke, K. / Pignot, M. / Goody, R.S. / Scheidig, A.J. / Weinhold, E. #2: ![]() Title: Differential binding of s-adenosylmethionine, s-adenosylhomocysteine and sinefungin to the adenine-specific DNA methyltransferase M.TaqI Authors: Schluckebier, G. / Kozak, M. / Bleimling, N. / Weinhold, E. / Saenger, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 123.5 KB | Display | ![]() |
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PDB format | ![]() | 89.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 777.4 KB | Display | ![]() |
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Full document | ![]() | 779.9 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 36.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2ih2C ![]() 2ih4C ![]() 1g38S 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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Unit cell |
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Details | The asymmetric unit contains one independent biological assembly consisting of M.TaqI, DNA and cofactor analog AETA. |
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Components
-DNA chain , 2 types, 2 molecules BC
#1: DNA chain | Mass: 3051.001 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid-phase DNA synthesis |
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#2: DNA chain | Mass: 2927.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Solid-phase DNA synthesis |
-Protein , 1 types, 1 molecules A
#3: Protein | Mass: 47931.195 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14385, site-specific DNA-methyltransferase (adenine-specific) |
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-Non-polymers , 3 types, 608 molecules ![](data/chem/img/NEA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-NEA / |
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#5: Chemical | ChemComp-GOL / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.88 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 3 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium ...Details: 3 microliters crystallization buffer (10 mM Tris/HCl, 300 mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100 mM KCl, 100 mM MgCl2, 6% isopropanol, 50 mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 13, 2005 / Details: ID14-3 (mirror) |
Radiation | Monochromator: ID14-3 (mirror) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.931 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→19.83 Å / Num. all: 45098 / Num. obs: 44043 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.31 % / Biso Wilson estimate: 23.58 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 12.54 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.37 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.4 / Num. unique all: 6656 / Rsym value: 0.427 / % possible all: 96.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1G38 Resolution: 1.8→19.82 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.516 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117 / 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: 19.69 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.82 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.846 Å / Total num. of bins used: 20
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