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Yorodumi- PDB-2f5i: X-ray structure of spermidine/spermine N1-acetyltransferase (SAT)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f5i | ||||||
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Title | X-ray structure of spermidine/spermine N1-acetyltransferase (SAT) from Homo sapiens | ||||||
Components | Diamine acetyltransferase 1 | ||||||
Keywords | TRANSFERASE / beta-alpha-barrels | ||||||
Function / homology | Function and homology information Interconversion of polyamines / spermidine acetylation / spermidine binding / putrescine catabolic process / polyamine biosynthetic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / N-acetyltransferase activity / angiogenesis / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SIR / Resolution: 2.3 Å | ||||||
Authors | Zhu, Y.Q. / Zhu, D.Y. / Vonrhein, C. / Wang, D.C. | ||||||
Citation | Journal: Proteins / Year: 2006 Title: Crystal structure of human spermidine/spermine N1-acetyltransferase (hSSAT): the first structure of a new sequence family of transferase homologous superfamily Authors: Zhu, Y.Q. / Zhu, D.Y. / Yin, L. / Zhang, Y. / Vonrhein, C. / Wang, D.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f5i.cif.gz | 87.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f5i.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 2f5i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f5i_validation.pdf.gz | 432.6 KB | Display | wwPDB validaton report |
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Full document | 2f5i_full_validation.pdf.gz | 442.2 KB | Display | |
Data in XML | 2f5i_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 2f5i_validation.cif.gz | 28.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f5/2f5i ftp://data.pdbj.org/pub/pdb/validation_reports/f5/2f5i | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21119.143 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(DE3) / References: UniProt: P21673, diamine N-acetyltransferase #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.08 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 8 Details: 3M NaCl , 0.1M TrisHCl, pH 8.0, VAPOR DIFFUSION, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 17156 / Num. obs: 15954 / % possible obs: 95.2 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.8 % / Biso Wilson estimate: 35.751 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.062 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 2.3→2.36 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 6.7 / Num. unique all: 900 / Rsym value: 0.14 / % possible all: 72.8 |
-Processing
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Refinement | Method to determine structure: SIR / Resolution: 2.3→25.2 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→25.2 Å
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Refine LS restraints |
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