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Yorodumi- PDB-1hmy: CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE COMPLEXED WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hmy | ||||||
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Title | CRYSTAL STRUCTURE OF THE HHAI DNA METHYLTRANSFERASE COMPLEXED WITH S-ADENOSYL-L-METHIONINE | ||||||
Components | HaeIII METHYLTRANSFERASE | ||||||
Keywords | TRANSFERASE(METHYLTRANSFERASE) | ||||||
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 / Resolution: 2.5 Å | ||||||
Authors | Cheng, X. | ||||||
Citation | 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. #1: Journal: Biochemistry / Year: 1992 Title: Purification, Crystallization, and Preliminary X-Ray Diffraction Analysis of an M.HhaI-Adomet Complex Authors: Kumar, S. / Cheng, X. / 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 | 1hmy.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hmy.ent.gz | 58.3 KB | Display | PDB format |
PDBx/mmJSON format | 1hmy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hm/1hmy ftp://data.pdbj.org/pub/pdb/validation_reports/hm/1hmy | 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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Atom site foot note | 1: CIS PROLINE - PRO 113 2: RESIDUES 85 - 91 ARE FLEXIBLE WITH HIGH TEMPERATURE FACTORS. |
-Components
#1: 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, DNA (cytosine-5-)-methyltransferase |
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#2: Chemical | ChemComp-SAM / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 4.82 Å3/Da / Density % sol: 74.48 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 16 ℃ / pH: 6.6 / Method: vapor diffusion, hanging drop / Details: referred to Biochemistry 31.8648-8653 1992 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.5 Å / Num. obs: 20981 / Num. measured all: 43292 / Rmerge(I) obs: 0.0719 |
-Processing
Software |
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Refinement | Rfactor Rwork: 0.2 / Rfactor obs: 0.2 / Highest resolution: 2.5 Å Details: RESIDUES 85 - 91 ARE FLEXIBLE WITH HIGH TEMPERATURE FACTORS. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.5 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2.5 Å / Lowest resolution: 8 Å / Num. reflection obs: 20057 / σ(F): 2 / Rfactor obs: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 1.82 |