[English] 日本語
Yorodumi- PDB-5ix3: Crystal structure of N-acetyltransferase from Staphylococcus aureus. -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ix3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of N-acetyltransferase from Staphylococcus aureus. | ||||||
Components | Diamine N-acetyltransferase | ||||||
Keywords | TRANSFERASE / N-acetyltransferase / GNATs / SPEG / Staphylococcus aureus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å | ||||||
Authors | Srivastava, P. / Khandokar, Y. / Forwood, J. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of N-acetyltransferase from Staphylococcus aureus. Authors: Srivastava, P. / Khandokar, Y. / Forwood, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5ix3.cif.gz | 51.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5ix3.ent.gz | 35.9 KB | Display | PDB format |
PDBx/mmJSON format | 5ix3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/5ix3 ftp://data.pdbj.org/pub/pdb/validation_reports/ix/5ix3 | HTTPS FTP |
---|
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 12||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
#1: Protein | Mass: 20078.924 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) Gene: res, speG, AL498_11440, ERS092844_02726, ERS195423_02759, R114_33, R92_33 Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: U5NVV0, diamine N-acetyltransferase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 54.98 % |
---|---|
Crystal grow | Temperature: 296 K / Method: vapor diffusion / pH: 8 / Details: 0.1M NaCl, 0.1M HEPES pH8.0, 1.6M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 15, 2015 |
Radiation | Monochromator: silicon double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→38 Å / Num. obs: 20350 / % possible obs: 97.4 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 13.19 |
Reflection shell | Resolution: 1.81→1.87 Å / Redundancy: 16.4 % / Rmerge(I) obs: 0.29 / % possible all: 95.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.81→37 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.389 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.166 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.81→37 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|