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Yorodumi- PDB-2zcj: Ternary structure of the Glu119Gln M.HhaI, C5-Cytosine DNA methyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2zcj | ||||||
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Title | Ternary structure of the Glu119Gln M.HhaI, C5-Cytosine DNA methyltransferase, with unmodified DNA and AdoHcy | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Alpha and beta / 3-layer Sandwich / Methyltransferase / Restriction system / S-adenosyl-L-methionine / 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 / simulation annealing / Resolution: 2.75 Å | ||||||
Authors | Shieh, F.K. / Reich, N.O. | ||||||
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 | 2zcj.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zcj.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 2zcj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zcj_validation.pdf.gz | 672.2 KB | Display | wwPDB validaton report |
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Full document | 2zcj_full_validation.pdf.gz | 685.4 KB | Display | |
Data in XML | 2zcj_validation.xml.gz | 16.8 KB | Display | |
Data in CIF | 2zcj_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/2zcj ftp://data.pdbj.org/pub/pdb/validation_reports/zc/2zcj | 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 / 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: 37041.223 Da / Num. of mol.: 1 / Mutation: E119Q 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) 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: 3.36 Å3/Da / Density % sol: 63.38 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM Sodium Citrate, 1.6-2.1 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 RU200 |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2006 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→10 Å / Num. obs: 18897 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.106 / Rsym value: 0.071 |
Reflection shell | Resolution: 2.6→2.75 Å / Rmerge(I) obs: 0.365 / Num. unique all: 2691 / Rsym value: 0.509 |
-Processing
Software |
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Refinement | Method to determine structure: simulation annealing / Resolution: 2.75→8.64 Å / σ(F): 2 / σ(I): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.75→8.64 Å
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LS refinement shell | Resolution: 2.75→2.78 Å /
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