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- PDB-1ky4: S-Adenosylhomocysteine hydrolase refined with noncrystallographic... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1ky4 | ||||||
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Title | S-Adenosylhomocysteine hydrolase refined with noncrystallographic restraints | ||||||
![]() | S-adenosylhomocysteine hydrolase | ||||||
![]() | HYDROLASE / S-adenosylhomocysteine | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Takata, Y. / Takusagawa, F. | ||||||
![]() | ![]() Title: Catalytic Mechanism of S-adenosylhomocysteine Hydrolase. Site-directed mutagenesis of Asp-130, Lys-185, Asp-189, and Asn-190. Authors: Takata, Y. / Yamada, T. / Huang, Y. / Komoto, J. / Gomi, T. / Ogawa, H. / Fujioka, M. / Takusagawa, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 331.5 KB | Display | ![]() |
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PDB format | ![]() | 267.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 705.7 KB | Display | ![]() |
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Full document | ![]() | 808.3 KB | Display | |
Data in XML | ![]() | 48.8 KB | Display | |
Data in CIF | ![]() | 68.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Details | The biological assembly is a homotetramer. |
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Components
#1: Protein | Mass: 47465.711 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-NAD / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.65 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: PEG 6000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 297K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃Details: used seeding, Komoto, J., (2000) J.Biol.Chem., 275, 32147. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jan 1, 1999 / Details: Yale mirror |
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→20 Å / Num. all: 58139 / Num. obs: 54797 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Rsym value: 0.071 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.8→2.92 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5 / Num. unique all: 5050 / Rsym value: 0.16 / % possible all: 87 |
Reflection | *PLUS Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS Rmerge(I) obs: 0.16 |
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Processing
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Refinement | Method to determine structure: ![]()
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Refine analyze | Luzzati coordinate error obs: 0.04 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→8 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement | *PLUS Num. reflection Rfree: 4950 / Rfactor all: 0.23 / Rfactor obs: 0.229 / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.228 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.3353 / Rfactor Rwork: 0.2821 |