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Yorodumi- PDB-1fjx: STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T2... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fjx | ||||||
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Title | STRUCTURE OF TERNARY COMPLEX OF HHAI METHYLTRANSFERASE MUTANT (T250G) IN COMPLEX WITH DNA AND ADOHCY | ||||||
Components |
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Keywords | TRANSFERASE/DNA / AdoMet-dependent Methyltransferase fold protein-DNA-cofactor complex / 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 haemolyticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 Å | ||||||
Authors | Vilkaitis, G. / Dong, A. / Weinhold, E. / Cheng, X. / Klimasauskas, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. Authors: Vilkaitis, G. / Dong, A. / Weinhold, E. / Cheng, X. / Klimasauskas, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fjx.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fjx.ent.gz | 92.8 KB | Display | PDB format |
PDBx/mmJSON format | 1fjx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/1fjx ftp://data.pdbj.org/pub/pdb/validation_reports/fj/1fjx | HTTPS FTP |
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-Related structure data
Related structure data | |
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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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Details | The biological assembly is a ternary complex from HhaI Methyltransferase, a palindromic oligonucleotide, and S-adenosyl-l-homocysteine (AdoHcy) |
-Components
#1: DNA chain | Mass: 3966.597 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically Synthesized #2: Protein | | Mass: 36998.156 Da / Num. of mol.: 1 / Mutation: T250G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus haemolyticus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P05102, EC: 2.1.1.73 #3: Chemical | #4: Chemical | ChemComp-SAH / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.33 Å3/Da / Density % sol: 63.1 % | ||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 2.7 M ammonium sulfate 20% (w/v) glucose 50 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 16K | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.26→20 Å / Num. all: 24152 / Num. obs: 67597 / % possible obs: 82.9 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.26→2.3 Å / Rmerge(I) obs: 0.288 / Num. unique all: 474 / % possible all: 32.7 |
Reflection | *PLUS Num. obs: 24152 / Num. measured all: 67597 |
-Processing
Software |
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Refinement | Resolution: 2.26→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 2.26→20 Å
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.207 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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