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Yorodumi- PDB-2ibs: Crystal structure of the adenine-specific DNA methyltransferase M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ibs | ||||||
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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 2-aminopurine at the target position | ||||||
Components |
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Keywords | TRANSFERASE/DNA / DNA / DNA methyltransferase / 2-aminopurine / base flipping / nucleotide flipping / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information 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 | Thermus aquaticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Pljevaljcic, G. / Lenz, T. / Scheidig, A.J. / Weinhold, E. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: 2-Aminopurine Flipped into the Active Site of the Adenine-Specific DNA Methyltransferase M.TaqI: Crystal Structures and Time-Resolved Fluorescence Authors: Lenz, T. / Bonnist, E.Y.M. / Pljevaljcic, G. / Neely, R.K. / Dryden, D.T.F. / Scheidig, A.J. / Jones, A.C. / Weinhold, E. #1: Journal: Nat.Struct.Biol. / Year: 2001 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: Journal: J.Mol.Biol. / Year: 1997 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ibs.cif.gz | 211.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ibs.ent.gz | 162 KB | Display | PDB format |
PDBx/mmJSON format | 2ibs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ibs_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 2ibs_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2ibs_validation.xml.gz | 38.1 KB | Display | |
Data in CIF | 2ibs_validation.cif.gz | 57.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ib/2ibs ftp://data.pdbj.org/pub/pdb/validation_reports/ib/2ibs | HTTPS FTP |
-Related structure data
Related structure data | 2ibtC 1g38S 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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2 |
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Unit cell |
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Details | The asymmetric unit contains two independent biological assemblies, each consisting of M.TaqI, DNA and cofactor analog AETA. |
-Components
#1: DNA chain | Mass: 3051.001 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Solid-phase DNA synthesis using commercially available phosphoramidites #2: DNA chain | Mass: 3052.046 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Solid-phase DNA synthesis using commercially available phosphoramidites #3: Protein | Mass: 47931.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus aquaticus (bacteria) / Strain: YT1 / Gene: taqIM / Plasmid: PA1/MTAQ-A49A / Production host: Escherichia coli (E. coli) / Strain (production host): ER2267 References: UniProt: P14385, site-specific DNA-methyltransferase (adenine-specific) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 3 microliters crystallization buffer (10mM Tris/HCl, 300mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100mM KCl, 100mM MgCl2, 6% isopropanol, 50mM sodium ...Details: 3 microliters crystallization buffer (10mM Tris/HCl, 300mM NaCl, pH 7.3) containing the complex plus 1 microliter reservoir solution (100mM KCl, 100mM MgCl2, 6% isopropanol, 50mM sodium cacodylate, pH 6.0), VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 13, 2001 / Details: mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→19.67 Å / Num. all: 36601 / Num. obs: 36299 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.69 % / Biso Wilson estimate: 25.27 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 9.33 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.63 / Num. unique all: 4175 / Rsym value: 0.334 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1G38 Resolution: 2.4→19.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.886 / SU B: 8.906 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.856 / ESU R Free: 0.297 / 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: 18.24 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→19.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.403→2.465 Å / Total num. of bins used: 20
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