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Yorodumi- PDB-4mht: TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH NATIVE DNA AND ADOHCY -
+Open data
-Basic information
Entry | Database: PDB / ID: 4mht | ||||||
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Title | TERNARY STRUCTURE OF HHAI METHYLTRANSFERASE WITH NATIVE DNA AND ADOHCY | ||||||
Components |
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Keywords | TRANSFERASE/DNA / COMPLEX (METHYLTRANSFERASE-DNA) / TRANSFERASE / METHYLTRANSFERASE / RESTRICTION SYSTEM / TRANSFERASE-DNA complex | ||||||
Function / homology | Function and homology information DNA (cytosine-5-)-methyltransferase / DNA (cytosine-5-)-methyltransferase activity / DNA restriction-modification system / methylation / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å | ||||||
Authors | Cheng, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes. Authors: O'Gara, M. / Klimasauskas, S. / Roberts, R.J. / Cheng, X. #1: 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. #2: 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 | 4mht.cif.gz | 98.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mht.ent.gz | 72.3 KB | Display | PDB format |
PDBx/mmJSON format | 4mht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4mht_validation.pdf.gz | 467.1 KB | Display | wwPDB validaton report |
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Full document | 4mht_full_validation.pdf.gz | 490.9 KB | Display | |
Data in XML | 4mht_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | 4mht_validation.cif.gz | 18 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mh/4mht ftp://data.pdbj.org/pub/pdb/validation_reports/mh/4mht | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 3676.431 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3980.624 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Protein | Mass: 37042.207 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Haemophilus haemolyticus (bacteria) / References: UniProt: P05102 |
#4: Chemical | ChemComp-SAH / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.06 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 5.6 / Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C |
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Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | % possible obs: 90 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 |
Reflection | *PLUS % possible obs: 90 % / Redundancy: 3.7 % |
-Processing
Software |
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Refinement | Resolution: 2.7→20 Å / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2.7→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.82 Å
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.7 Å / Lowest resolution: 20 Å / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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