+Open data
-Basic information
Entry | Database: PDB / ID: 5axd | ||||||
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Title | Crystal structure of mouse SAHH complexed with ribavirin | ||||||
Components | Adenosylhomocysteinase | ||||||
Keywords | HYDROLASE / hydrolase nucleoside complex | ||||||
Function / homology | Function and homology information Sulfur amino acid metabolism / S-adenosylhomocysteine catabolic process / Methylation / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / response to nutrient ...Sulfur amino acid metabolism / S-adenosylhomocysteine catabolic process / Methylation / circadian sleep/wake cycle / adenyl nucleotide binding / chronic inflammatory response to antigenic stimulus / adenosylhomocysteinase / S-adenosylmethionine cycle / adenosylhomocysteinase activity / response to nutrient / NAD binding / : / melanosome / one-carbon metabolic process / copper ion binding / endoplasmic reticulum / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6 Å | ||||||
Authors | Kusakabe, Y. / Ishihara, M. / Tanaka, N. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of mouse SAHH complexed with ribavirin Authors: Kusakabe, Y. / Ishihara, M. / Tanaka, N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5axd.cif.gz | 206.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5axd.ent.gz | 162.7 KB | Display | PDB format |
PDBx/mmJSON format | 5axd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/5axd ftp://data.pdbj.org/pub/pdb/validation_reports/ax/5axd | 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: 47746.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ahcy / Production host: Escherichia coli (E. coli) / References: UniProt: P50247, adenosylhomocysteinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.55 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 12, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. obs: 121803 / % possible obs: 99.6 % / Redundancy: 5.4 % / Rsym value: 0.099 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.474 / Mean I/σ(I) obs: 3.5 / % possible all: 99.6 |
-Processing
Software | Name: REFMAC / Version: 5.5.0110 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.267 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.414 Å2
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Refinement step | Cycle: 1 / Resolution: 1.6→50 Å
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