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Yorodumi- PDB-1yfl: T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1yfl | ||||||
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Title | T4Dam in Complex with Sinefungin and 16-mer Oligonucleotide Showing Semi-specific and Specific Contact and Flipped Base | ||||||
Components |
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Keywords | TRANSFERASE/DNA / T4DAM / METHYLTRANSFERASE / DNA / PROTEIN-DNA COMPLEX / BASE-FLIPPING / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information symbiont-mediated evasion of host restriction-modification system / DNA-methyltransferase activity / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / methylation / DNA replication / DNA binding Similarity search - Function | ||||||
Biological species | Enterobacteria phage T4 (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å | ||||||
Authors | Horton, J.R. / Liebert, K. / Hattman, S. / Jeltsch, A. / Cheng, X. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2005 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: Journal: Nat.Struct.Mol.Biol. / Year: 2003 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1yfl.cif.gz | 246 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1yfl.ent.gz | 193.7 KB | Display | PDB format |
PDBx/mmJSON format | 1yfl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yf/1yfl ftp://data.pdbj.org/pub/pdb/validation_reports/yf/1yfl | HTTPS FTP |
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-Related structure data
Related structure data | 1yf3C 1yfjC 1q0sS 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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1 |
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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 4898.192 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthesized by New England Biolabs #2: Protein | Mass: 30461.898 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: DAM / Plasmid: pJW2 / Production host: Escherichia coli (E. coli) / Strain (production host): GM 2971 References: UniProt: P04392, site-specific DNA-methyltransferase (adenine-specific) #3: Chemical | ChemComp-SFG / #4: 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: 3.15 Å3/Da / Density % sol: 64.2 % | ||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: PEG 6000, MES, ammonium acetate, CaCl2, glycerol, pH 6.2, 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: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: AREA DETECTOR / Date: Jun 6, 2004 |
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: 3.09→30 Å / Num. obs: 33149 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 54.4 Å2 / Rsym value: 0.081 / Net I/σ(I): 18.7 |
Reflection shell | Resolution: 3.09→3.2 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 5.8 / Num. unique all: 3302 / Rsym value: 0.314 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Q0S Resolution: 3.09→29.4 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The crystal of T4Dam-sinefungin-16mer DNA can also be indexed in the space group P43, with the same cell dimensions but two protein molecules and two half DNA molecules in the asymmetric ...Details: The crystal of T4Dam-sinefungin-16mer DNA can also be indexed in the space group P43, with the same cell dimensions but two protein molecules and two half DNA molecules in the asymmetric unit. The DNA axis is in parallel with the crystallographic z-axis (a 4-fold screw axis). To have a complete DNA molecule, we indexed the diffraction data in a lower symmetry space group P21. The two protein molecules along the DNA axis were constrained during the refinement by non-crystallographic 4-fold screw symmetry.
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Displacement parameters | Biso mean: 57.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.09→29.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.09→3.2 Å / Rfactor Rfree error: 0.033
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