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Open data
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Basic information
Entry | Database: PDB / ID: 1g38 | ||||||
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Title | ADENINE-SPECIFIC METHYLTRANSFERASE M. TAQ I/DNA COMPLEX | ||||||
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![]() | TRANSFERASE/DNA / TRANSFERASE / DNA / METHYLTRANSFERASE / RESTRICTION SYSTEM / 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 | ![]() ![]() | ||||||
![]() | Goedecke, K. / Pignot, M. / Goody, R.S. / Scheidig, A.J. / Weinhold, E. | ||||||
![]() | ![]() 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. #1: ![]() Title: DIFFERENTIAL BINDING OF S-ADENOSYLMETHIONINE, S-ADENOSYLHOMOCYSTEINE AND SINEFUNGIN TO THE ADENINE-SPECIFIC DNA METHYLTRANSFERASE M. TAQ I 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 | ![]() | 205.5 KB | Display | ![]() |
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PDB format | ![]() | 157.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 36.9 KB | Display | |
Data in CIF | ![]() | 53.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2admS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: DNA chain | Mass: 3051.001 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: DNA chain | Mass: 3052.046 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: Protein | Mass: 44979.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 21 - 413 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14385, site-specific DNA-methyltransferase (adenine-specific) #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 43.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 15% Isopropanol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | Name: isopropanol | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 7, 1999 / Details: mirror |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 218047 / Num. obs: 54457 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 6.1 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 10.42 |
Reflection shell | Resolution: 2→2.13 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.6 / Num. unique all: 8013 / Rsym value: 0.195 / % possible all: 67.1 |
Reflection | *PLUS Num. measured all: 218047 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2ADM Resolution: 2→20 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: isotropic / Cross valid method: CNS throughout / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 15.5 Å2 | |||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: CNS / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / Num. reflection all: 54457 / σ(F): 0 / % reflection Rfree: 10.2 % / Rfactor obs: 0.196 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 15.5 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.276 / % reflection Rfree: 10.3 % / Rfactor Rwork: 0.219 |