[English] 日本語
Yorodumi- PDB-2bkk: Crystal structure of Aminoglycoside Phosphotransferase APH(3')-II... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bkk | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a | ||||||
Components |
| ||||||
Keywords | TRANSFERASE/PEPTIDE / TRANSFERASE-DESIGNED PROTEIN COMPLEX / ANKYRIN REPEAT / CO-CRYSTALLIZATION / INHIBITOR DESIGN / DRUG DESIGN / ENZYME INHIBITION / KINASE INHIBITION / DESIGNED REPEAT PROTEIN / ANTIBIOTIC RESISTANCE / ATP-BINDING / KINASE / PLASMID / TRANSFERASE / TRANSFERASE-PEPTIDE complex | ||||||
Function / homology | Function and homology information kanamycin kinase / kanamycin kinase activity / phosphorylation / response to antibiotic / ATP binding Similarity search - Function | ||||||
Biological species | ENTEROCOCCUS FAECALIS (bacteria) SYNTHETIC CONSTRUCT (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Kohl, A. / Amstutz, P. / Parizek, P. / Binz, H.K. / Briand, C. / Capitani, G. / Forrer, P. / Pluckthun, A. / Grutter, M.G. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Allosteric Inhibition of Aminoglycoside Phosphotransferase by a Designed Ankyrin Repeat Protein Authors: Kohl, A. / Amstutz, P. / Parizek, P. / Binz, H.K. / Briand, C. / Capitani, G. / Forrer, P. / Pluckthun, A. / Grutter, M.G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bkk.cif.gz | 187.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bkk.ent.gz | 147.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bkk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/2bkk ftp://data.pdbj.org/pub/pdb/validation_reports/bk/2bkk | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 30979.916 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Description: STREPTOCOCCUS FAECALIS, STAPHYLOCOCCUS AUREUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P00554, UniProt: P0A3Y5*PLUS, kanamycin kinase #2: Protein | Mass: 18602.836 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Production host: ESCHERICHIA COLI (E. coli) #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Compound details | FUNCTION: RESISTANCE | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41 % |
---|---|
Crystal grow | Details: 15-20 % PEG 5500, 0.1 M MES PH 5.9-6.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9 |
Detector | Type: MARRESEARCH / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→20 Å / Num. obs: 46440 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.05 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRIES 1MJO, 1J7L Resolution: 2.15→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THERE ARE TWO INDEPENDENT COMPLEXES AB AND CD IN THE ASYMMETRIC UNIT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.8 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|