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- PDB-1yfj: T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing S... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1yfj | ||||||
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Title | T4Dam in Complex with AdoHcy and 15-mer Oligonucleotide Showing Semi-specific and Specific Contact | ||||||
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![]() | TRANSFERASE/DNA / T4DAM / METHYLTRANSFERASE / DNA / PROTEIN-DNA COMPLEX / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | ![]() symbiont-mediated evasion of host restriction-modification system / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / DNA restriction-modification system / mismatch repair / methylation / DNA replication / sequence-specific DNA binding ...symbiont-mediated evasion of host restriction-modification system / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / DNA restriction-modification system / mismatch repair / methylation / DNA replication / sequence-specific DNA binding / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horton, J.R. / Liebert, K. / Hattman, S. / Jeltsch, A. / Cheng, X. | ||||||
![]() | ![]() Title: Transition from Nonspecific to Specific DNA Interactions along the Substrate-Recognition Pathway of Dam Methyltransferase. Authors: Horton, J.R. / Liebert, K. / Hattman, S. / Jeltsch, A. / Cheng, X. #1: ![]() Title: Structure of the bacteriophage T4 DNA adenine methyltransferase Authors: Yang, Z. / Horton, J.R. / Zhou, L. / Zhang, X.J. / Dong, A. / Zhang, X. / Schlagman, S.L. / Kossykh, V. / Cheng, X. | ||||||
History |
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Remark 999 | SEQUENCE 1) Author states that Q139R, Y140F and Q209L reflect conflicts between deposited protein ...SEQUENCE 1) Author states that Q139R, Y140F and Q209L reflect conflicts between deposited protein sequence and translated deposited DNA-->protein sequence. From their electron density, it appears the translated DNA sequence is correct ; 2) It is possible residue 119 could be a Tyr rather than Asp based on some electron density evidence. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 395.4 KB | Display | ![]() |
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PDB format | ![]() | 307.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1yf3C ![]() 1yflC ![]() 1q0sS 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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3 | ![]()
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4 | ![]()
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5 | ![]()
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6 | ![]()
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Unit cell |
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Components
-DNA chain / Protein , 2 types, 16 molecules 1234567890ABCDEF
#1: DNA chain | Mass: 4584.985 Da / Num. of mol.: 10 / Source method: obtained synthetically / Details: Synthesized by New England Biolabs #2: Protein | Mass: 30461.898 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04392, site-specific DNA-methyltransferase (adenine-specific) |
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-Non-polymers , 4 types, 355 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | ChemComp-SAH / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.24 Å3/Da / Density % sol: 65.1 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES, ammonium acetate, CaCl2, and ethyleneglycol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 173 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 8, 2003 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→35 Å / Num. obs: 78518 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 28.9 Å2 / Rsym value: 0.07 / Net I/σ(I): 12.9 |
Reflection shell | Resolution: 2.69→2.79 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 7.1 / Num. unique all: 7801 / Rsym value: 0.323 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1Q0S Resolution: 2.69→34.78 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 55.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.69→34.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.79 Å / Rfactor Rfree error: 0.018
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