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Yorodumi- PDB-8fv0: SpeG spermidine N-acetyltransferase from Staphylococcus aureus in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8fv0 | |||||||||
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Title | SpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine | |||||||||
Components | Diamine N-acetyltransferase | |||||||||
Keywords | TRANSFERASE | |||||||||
Function / homology | diamine N-acetyltransferase activity / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / SPERMINE / Diamine N-acetyltransferase Function and homology information | |||||||||
Biological species | Staphylococcus aureus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å | |||||||||
Authors | Tsimbalyuk, S. / Forwood, J.K. | |||||||||
Funding support | 1items
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Citation | Journal: To Be Published Title: SpeG spermidine N-acetyltransferase from Staphylococcus aureus in complex with spermine Authors: Tsimbalyuk, S. / Forwood, J.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8fv0.cif.gz | 243.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8fv0.ent.gz | 165.1 KB | Display | PDB format |
PDBx/mmJSON format | 8fv0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fv/8fv0 ftp://data.pdbj.org/pub/pdb/validation_reports/fv/8fv0 | HTTPS FTP |
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-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 20077.939 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: res / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: U5NVV0 #2: Chemical | Has ligand of interest | N | |
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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: 50.14 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M NaCl, 0.1 M HEPES pH 8.0, and 1.6 M ammonium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.65→24.86 Å / Num. obs: 17700 / % possible obs: 99.9 % / Redundancy: 7.5 % / Biso Wilson estimate: 41.04 Å2 / CC1/2: 0.775 / Rmerge(I) obs: 0.14 / Net I/σ(I): 2.4 |
Reflection shell | Resolution: 2.64→2.65 Å / Num. unique obs: 871 / CC1/2: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→24.86 Å / SU ML: 0.2748 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2879 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→24.86 Å
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Refine LS restraints |
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LS refinement shell |
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