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Yorodumi- PDB-1mht: COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-A... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1mht | ||||||
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Title | COVALENT TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE, DNA AND S-ADENOSYL-L-HOMOCYSTEINE | ||||||
Components |
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Keywords | TRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DOUBLE HELIX / OVERHANGING BASE / FLIPPED-OUT BASE / MODIFIED / TRANSFERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å | ||||||
Authors | Cheng, X. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1994 Title: HhaI methyltransferase flips its target base out of the DNA helix. Authors: Klimasauskas, S. / Kumar, S. / Roberts, R.J. / Cheng, X. #1: Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: Crystal Structure of the HhaI DNA Methyltransferase Complexed with S-Adenosyl-L-Methionine Authors: Cheng, X. / Kumar, S. / Posfai, J. / Pflugrath, J.W. / Roberts, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mht.cif.gz | 89.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mht.ent.gz | 70.6 KB | Display | PDB format |
PDBx/mmJSON format | 1mht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/1mht ftp://data.pdbj.org/pub/pdb/validation_reports/mh/1mht | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3712.436 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 4016.629 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 37042.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / References: UniProt: P05102, EC: 2.1.1.73 |
#4: Chemical | ChemComp-SAH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.51 Å3/Da / Density % sol: 65 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.25 Details: BIS-TRIS-PROPANE_HCL, NACL, EDTA, pH 7.25, VAPOR DIFFUSION, HANGING DROP, temperature 289.00K | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal grow | *PLUS Temperature: 16 ℃ | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Type: NSLS / Wavelength: 1 |
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Detector | Type: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.8 Å / Num. obs: 17839 / Rmerge(I) obs: 0.0765 |
Reflection | *PLUS Highest resolution: 2.8 Å |
-Processing
Software |
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Refinement | Resolution: 2.6→10 Å /
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Refinement step | Cycle: LAST / Resolution: 2.6→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.6 |