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Yorodumi- PDB-3bj8: Spermine/spermidine N1-acetyltransferase from mouse: Crystal stru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bj8 | ||||||
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Title | Spermine/spermidine N1-acetyltransferase from mouse: Crystal structure of a ternary complex reveals solvent-mediated spermine binding | ||||||
Components | Diamine acetyltransferase 1 | ||||||
Keywords | TRANSFERASE / SSAT / CoA / Spermine / Ternary complex / Acyltransferase / Cytoplasm | ||||||
Function / homology | Function and homology information Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine metabolic process / spermine catabolic process / polyamine biosynthetic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / polyamine catabolic process ...Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine metabolic process / spermine catabolic process / polyamine biosynthetic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / polyamine catabolic process / N-acetyltransferase activity / regulation of cell population proliferation / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Montemayor, E.J. / Hoffman, D.W. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: The crystal structure of spermidine/spermine N1-acetyltransferase in complex with spermine provides insights into substrate binding and catalysis. Authors: Montemayor, E.J. / Hoffman, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bj8.cif.gz | 143.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bj8.ent.gz | 121.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bj8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bj8_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 3bj8_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 3bj8_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 3bj8_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bj/3bj8 ftp://data.pdbj.org/pub/pdb/validation_reports/bj/3bj8 | HTTPS FTP |
-Related 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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-Components
#1: Protein | Mass: 20036.943 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Sat1, Sat / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P48026, diamine N-acetyltransferase #2: Chemical | ChemComp-COA / #3: Chemical | ChemComp-SPM / | #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: 2.47 Å3/Da / Density % sol: 50.18 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9 Details: pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 15, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→39 Å / Num. all: 35462 / Num. obs: 35462 / Biso Wilson estimate: 23.3 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→33.98 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1261162.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.2484 Å2 / ksol: 0.340782 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.3→33.98 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.44 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
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Xplor file |
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