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Yorodumi- PDB-2z6a: S-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Pre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2z6a | ||||||
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Title | S-Adenosyl-L-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation | ||||||
Components |
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Keywords | TRANSFERASE/DNA / Protein-DNA 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 / methylation / DNA binding Similarity search - Function | ||||||
Biological species | Haemophilus parahaemolyticus (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / Simulation annealing / Resolution: 2.88 Å | ||||||
Authors | Shieh, F.K. | ||||||
Citation | Journal: Biochemistry / Year: 2007 Title: S-Adenosyl-l-methionine-Dependent Methyl Transfer: Observable Precatalytic Intermediates during DNA Cytosine Methylation Authors: Youngblood, B. / Shieh, F.K. / Buller, F. / Bullock, T. / 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 | 2z6a.cif.gz | 95.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2z6a.ent.gz | 69.3 KB | Display | PDB format |
PDBx/mmJSON format | 2z6a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2z6a_validation.pdf.gz | 699.5 KB | Display | wwPDB validaton report |
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Full document | 2z6a_full_validation.pdf.gz | 718 KB | Display | |
Data in XML | 2z6a_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 2z6a_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z6/2z6a ftp://data.pdbj.org/pub/pdb/validation_reports/z6/2z6a | HTTPS FTP |
-Related structure data
Related structure data | 2hr1S S: Starting model for refinement |
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Similar 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 / Source: (synth.) synthetic construct (others) |
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#2: DNA chain | Mass: 3966.597 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: Protein | Mass: 37010.145 Da / Num. of mol.: 1 / Mutation: C81A 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: 3.38 Å3/Da / Density % sol: 63.65 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2.0M Ammonium Sulfate, 50mM Sodium Citrate, pH 6.5, 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 RU300 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 180 mm plate / Detector: IMAGE PLATE / Date: Dec 1, 2005 / 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: 2.88→20 Å / Num. obs: 14120 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 65.6 Å2 / Rmerge(I) obs: 0.16 / Rsym value: 0.09 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.88→2.98 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / Num. unique all: 2034 / Rsym value: 0.354 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: Simulation annealing Starting model: PDB Entry 2HR1 Resolution: 2.88→8.85 Å / σ(F): 2 / σ(I): 2
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Refinement step | Cycle: LAST / Resolution: 2.88→8.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.88→2.92 Å / Rfactor Rfree error: 0.03
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