[English] 日本語
![](img/lk-miru.gif)
- PDB-1yf3: T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making No... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1yf3 | ||||||
---|---|---|---|---|---|---|---|
Title | T4Dam in Complex with AdoHcy and 13-mer Oligonucleotide Making Non- and Semi-specific (~1/4) Contact | ||||||
![]() |
| ||||||
![]() | Transferase/DNA / T4DAM / METHYLTRANSFERASE / DNA / 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 / mismatch repair / methylation / DNA replication / sequence-specific DNA binding / 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 |
| ||||||
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) Residue 119 were modeled (for both A and B) as Tyr in this structure as the electron density does not support an Asp here. The electron denstiy for B119 fits a Tyr residue perfectly. |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 137.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 102.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 525.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 537.7 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1yfjC ![]() 1yflC ![]() 1q0sS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-DNA chain , 2 types, 2 molecules CD
#1: DNA chain | Mass: 3935.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by New England Biolabs |
---|---|
#2: DNA chain | Mass: 4006.621 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthesized by New England Biolabs |
-Protein , 1 types, 2 molecules AB
#3: Protein | Mass: 30509.988 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P04392, site-specific DNA-methyltransferase (adenine-specific) |
---|
-Non-polymers , 3 types, 208 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.9 % | ||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.4 Details: PEG MME 5000, citrate-phosphate, ammonium sulphate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||
Components of the solutions |
|
-Data collection
Diffraction | Mean temperature: 173 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2003 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.2826 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→28 Å / Num. obs: 29474 / % possible obs: 95.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 30 Å2 / Rsym value: 0.047 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 2.29→2.37 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 9.6 / Rsym value: 0.187 / % possible all: 97.3 |
-
Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1Q0S Resolution: 2.29→28 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.8 Å2
| |||||||||||||||||||||||||
Refine analyze |
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→28 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.29→2.37 Å / Rfactor Rfree error: 0.023
|