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Yorodumi- PDB-1d4f: CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d4f | ||||||
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Title | CRYSTAL STRUCTURE OF RECOMBINANT RAT-LIVER D244E MUTANT S-ADENOSYLHOMOCYSTEINE HYDROLASE | ||||||
Components | S-ADENOSYLHOMOCYSTEINE HYDROLASE | ||||||
Keywords | HYDROLASE / S-adenosylhomocysteine hydrolase / AdoHcyase / AdoHcy / Mutagenesis / X-ray crystal structure / Enzyme structure | ||||||
Function / homology | Function and homology information adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / Methylation ...adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / Methylation / response to nutrient / NAD binding / protein self-association / melanosome / one-carbon metabolic process / response to hypoxia / copper ion binding / endoplasmic reticulum / nucleus / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.8 Å | ||||||
Authors | Komoto, J. / Huang, Y. / Takusagawa, F. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Effects of site-directed mutagenesis on structure and function of recombinant rat liver S-adenosylhomocysteine hydrolase. Crystal structure of D244E mutant enzyme. Authors: Komoto, J. / Huang, Y. / Gomi, T. / Ogawa, H. / Takata, Y. / Fujioka, M. / Takusagawa, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d4f.cif.gz | 342.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d4f.ent.gz | 278.9 KB | Display | PDB format |
PDBx/mmJSON format | 1d4f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d4/1d4f ftp://data.pdbj.org/pub/pdb/validation_reports/d4/1d4f | 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 47479.738 Da / Num. of mol.: 4 / Mutation: D244E Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: LIVER / Production host: Escherichia coli (E. coli) / References: UniProt: P10760, adenosylhomocysteinase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-ADN / #4: 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: 2.44 Å3/Da / Density % sol: 49.51 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 22% PEG 4000, 50 mM Tris/HCl, 2% glycerol, 10% isopropanol, and 1 mM DTT. Protein concentration is 10 mg/mL., pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Details: used seeding | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Nov 27, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→8 Å / Num. all: 241990 / Num. obs: 241990 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 24.4 |
Reflection shell | Resolution: 2.8→2.9 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.265 / Num. unique all: 3808 / % possible all: 83.7 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. obs: 43000 / % possible obs: 85.6 % / Num. measured all: 241990 / Rmerge(I) obs: 0.093 |
-Processing
Software |
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Refinement | Resolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 8 Å / σ(F): 0 / % reflection Rfree: 10 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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