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- PDB-7qw6: Adenine-specific DNA methyltransferase M.BseCI complexed with Ado... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qw6 | ||||||
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Title | Adenine-specific DNA methyltransferase M.BseCI complexed with AdoHcy and cognate hemimethylated DNA duplex | ||||||
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![]() | TRANSFERASE / Methyltransferase / DNA-modification / Adenine-N6 methylation / Base flipping | ||||||
Function / homology | ![]() N-methyltransferase activity / 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 | ![]() ![]() ![]() | ||||||
![]() | Mitsikas, D.A. / Kouyianou, K. / Kotsifaki, D. / Providaki, M. / Bouriotis, V. / Glykos, N.M. / Kokkinidis, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of M.BseCI DNA methyltransferase from Geobacillus stearothermophilus. Authors: Mitsikas, D.A. / Kouyianou, K. / Kotsifaki, D. / Providaki, M. / Bouriotis, V. / Glykos, N.M. / Kokkinidis, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 299.4 KB | Display | ![]() |
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PDB format | ![]() | 210.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 693.8 KB | Display | ![]() |
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Full document | ![]() | 696.2 KB | Display | |
Data in XML | ![]() | 23.6 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7qw5SC ![]() 7qw7C ![]() 7qw8C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 67761.094 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: bseCIM / Production host: ![]() ![]() References: UniProt: P43423, site-specific DNA-methyltransferase (adenine-specific) |
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#2: DNA chain | Mass: 3045.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#3: DNA chain | Mass: 3059.031 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#4: Chemical | ChemComp-SAH / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.5 / Details: Glycerol ethoxylate, Tris-HCl, paraffin oil |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→52.03 Å / Num. obs: 24491 / % possible obs: 92.4 % / Redundancy: 5.3 % / Biso Wilson estimate: 54.29 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.048 / Rrim(I) all: 0.12 / Χ2: 1.03 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2662 / Rpim(I) all: 0.431 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7QW5 Resolution: 2.4→42.93 Å / SU ML: 0.2904 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.0864 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.2 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.94 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→42.93 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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