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Yorodumi- PDB-2z6u: Ternary structure of the Glu119Ala M.HhaI, C5-Cytosine DNA methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6u | ||||||
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Title | Ternary structure of the Glu119Ala M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy | ||||||
Components |
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Keywords | TRANSFERASE/DNA / beta-alpha-Complex / Methyltransferase / Restriction system / S-adenosyl-L-methionine / Transferase / 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 parahaemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Simulation Annealing / Resolution: 2.72 Å | ||||||
Authors | Shieh, F.K. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: AdoMet-dependent Methyl-transfer: Glu(119) Is Essential for DNA C5-Cytosine Methyltransferase M.HhaI Authors: Shieh, F.K. / 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 | 2z6u.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6u.ent.gz | 70.4 KB | Display | PDB format |
PDBx/mmJSON format | 2z6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6u ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6u | HTTPS FTP |
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-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 / Details: Synthetic Construction |
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#2: DNA chain | Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Construction |
#3: Protein | Mass: 36984.172 Da / Num. of mol.: 1 / Mutation: E119A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria) Gene: hhaIM / Plasmid: pHSHW-5 / Production host: Escherichia coli (E. coli) / Strain (production host): ER1727 References: UniProt: P05102, DNA (cytosine-5-)-methyltransferase |
#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: 63.46 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100mM sodium citrate buffer, 45%-55% 3.5M ammonium sulfate, 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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 2006 / Details: mirrors |
Radiation | Monochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→10 Å / Num. obs: 16916 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.5 % / Rmerge(I) obs: 0.091 / Rsym value: 0.072 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 10.2 / Num. unique all: 1120 / Rsym value: 0.373 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: Simulation Annealing / Resolution: 2.72→10 Å / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 2.72→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.72→2.75 Å
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