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Yorodumi- PDB-1k0u: Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar"... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1k0u | |||||||||
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Title | Inhibition of S-adenosylhomocysteine Hydrolase by "acyclic sugar" Adenosine Analogue D-eritadenine | |||||||||
Components | S-ADENOSYL-L-HOMOCYSTEINE HYDROLASE | |||||||||
Keywords | HYDROLASE / S-adenosylhomocysteine / D-eritadenine / inhibitor | |||||||||
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 / adenosylhomocysteinase activity / Methylation / S-adenosylmethionine cycle ...adenosylselenohomocysteinase activity / S-adenosylhomocysteine catabolic process / Sulfur amino acid metabolism / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / adenosylhomocysteinase activity / Methylation / S-adenosylmethionine cycle / response to nutrient / NAD binding / melanosome / one-carbon metabolic process / response to hypoxia / copper ion binding / endoplasmic reticulum / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | |||||||||
Authors | Takusagawa, F. / Huang, Y. / Komoto, J. / Takata, Y. / Gomi, T. / Ogawa, H. / Fujioka, M. / Powell, D. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Inhibition of S-adenosylhomocysteine hydrolase by acyclic sugar adenosine analogue D-eritadenine. Crystal structure of S-adenosylhomocysteine hydrolase complexed with D-eritadenine. Authors: Huang, Y. / Komoto, J. / Takata, Y. / Powell, D.R. / Gomi, T. / Ogawa, H. / 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 | 1k0u.cif.gz | 630.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1k0u.ent.gz | 517.3 KB | Display | PDB format |
PDBx/mmJSON format | 1k0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1k0u_validation.pdf.gz | 4.4 MB | Display | wwPDB validaton report |
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Full document | 1k0u_full_validation.pdf.gz | 4.6 MB | Display | |
Data in XML | 1k0u_validation.xml.gz | 146.1 KB | Display | |
Data in CIF | 1k0u_validation.cif.gz | 188 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k0/1k0u ftp://data.pdbj.org/pub/pdb/validation_reports/k0/1k0u | HTTPS FTP |
-Related structure data
Related structure data | 1d4fS 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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2 |
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Unit cell |
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Details | The asymmetric unit contains two tetrameric enzymes, i.e., contains eight identical subunits. |
-Components
#1: Protein | Mass: 47465.711 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P10760, adenosylhomocysteinase #2: Chemical | ChemComp-NAD / #3: Chemical | ChemComp-DEA / #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: 2.24 Å3/Da / Density % sol: 45.17 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ | ||||||||||||||||||||||||||||||
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 Å |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 20, 1999 / 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: 3→10 Å / Num. all: 59076 / Num. obs: 56933 / % possible obs: 85 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 2.1 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 6.2 |
Reflection shell | Resolution: 3→3.1 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.19 / % possible all: 82 |
Reflection | *PLUS Lowest resolution: 10 Å / Num. obs: 59048 / % possible obs: 91.5 % / Num. measured all: 241990 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1D4F Resolution: 3→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 5.3 Å2
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Refine analyze | Luzzati sigma a obs: 0.34 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→10 Å / Rfactor Rfree error: 0.01
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / σ(F): 2 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 5.3 Å2 | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 10 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.208 |