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Yorodumi- PDB-2hr1: Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2hr1 | ||||||
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Title | Ternary structure of WT M.HhaI C5-Cytosine DNA methyltransferase with unmodified DNA and AdoHcy | ||||||
Components |
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Keywords | Transferase/DNA / High resolution / M.HhaI / 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 parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Simulation Annealling / Resolution: 1.96 Å | ||||||
Authors | Shieh, F. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: The Role of Arg165 Towards Base Flipping, Base Stabilization and Catalysis in M.HhaI. Authors: Shieh, F.K. / Youngblood, B. / Reich, N.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hr1.cif.gz | 96.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hr1.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 2hr1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2hr1_validation.pdf.gz | 713.4 KB | Display | wwPDB validaton report |
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Full document | 2hr1_full_validation.pdf.gz | 723.3 KB | Display | |
Data in XML | 2hr1_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 2hr1_validation.cif.gz | 24.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/2hr1 ftp://data.pdbj.org/pub/pdb/validation_reports/hr/2hr1 | 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: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: DNA chain | Mass: 3966.597 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 parahaemolyticus (bacteria) Gene: hhaIM / Production host: Escherichia coli (E. coli) / Strain (production host): ER172 / References: UniProt: P05102, EC: 2.1.1.73 |
#4: Chemical | ChemComp-SAH / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.37 Å3/Da / Density % sol: 63.45 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: Ammonium Sulfate 15%, Sodium Citrate 100 mM, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K | ||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 9, 2005 |
Radiation | Monochromator: Bragg reflection / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→8.05 Å / Num. obs: 51122 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.9 |
Reflection shell | Resolution: 1.8→1.85 Å / % possible all: 72.3 |
-Processing
Software |
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Refinement | Method to determine structure: Simulation Annealling / Resolution: 1.96→2.01 Å / σ(F): 1.9 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.96→2.01 Å
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Refine LS restraints |
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