[English] 日本語
Yorodumi- PDB-5iqf: Aminoglycoside Phosphotransferase (2'')-Ia (CTD of APH(6')-Ie/APH... -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 5iqf | ||||||
|---|---|---|---|---|---|---|---|
| Title | Aminoglycoside Phosphotransferase (2'')-Ia (CTD of APH(6')-Ie/APH(2'')-Ia) in complex with GDP and Magnesium | ||||||
Components | Bifunctional AAC/APH | ||||||
Keywords | TRANSFERASE / Kinase / Antibiotic / Aminoglycoside / Resistance | ||||||
| Function / homology | Function and homology informationaminoglycoside 2''-phosphotransferase / aminoglycoside phosphotransferase activity / N-acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / ATP binding / cytoplasm Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.35 Å | ||||||
Authors | Caldwell, S.J. / Berghuis, A.M. | ||||||
| Funding support | Canada, 1items
| ||||||
Citation | Journal: Structure / Year: 2016Title: Antibiotic Binding Drives Catalytic Activation of Aminoglycoside Kinase APH(2)-Ia. Authors: Caldwell, S.J. / Huang, Y. / Berghuis, A.M. | ||||||
| History |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 5iqf.cif.gz | 534.5 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb5iqf.ent.gz | 439.6 KB | Display | PDB format |
| PDBx/mmJSON format | 5iqf.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5iqf_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 5iqf_full_validation.pdf.gz | 1.6 MB | Display | |
| Data in XML | 5iqf_validation.xml.gz | 53.8 KB | Display | |
| Data in CIF | 5iqf_validation.cif.gz | 77.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqf ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqf | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5bylSC ![]() 5iqaC ![]() 5iqbC ![]() 5iqcC ![]() 5iqdC ![]() 5iqeC ![]() 5iqgC ![]() 5iqhC ![]() 5iqiC S: Starting model for refinement C: citing same article ( |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 3 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 4 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
|
-
Components
-Protein , 1 types, 4 molecules ABCD
| #1: Protein | Mass: 35948.199 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 175-479) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P0A0C1, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
|---|
-Non-polymers , 5 types, 937 molecules 








| #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.78 Å3/Da / Density % sol: 55.71 % |
|---|---|
| Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 80-120mM MgCl2, 8% glycerol, 10% PEG 3350, 100mM HEPES pH 7.5 |
-Data collection
| Diffraction | Mean temperature: 100 K |
|---|---|
| Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å |
| Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 10, 2016 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
| Reflection | Resolution: 2.35→89.13 Å / Num. obs: 65601 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 35.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.9 |
| Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 6.9 % / Rmerge(I) obs: 1.211 / Mean I/σ(I) obs: 1.7 / % possible all: 100 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: FOURIER SYNTHESISStarting model: 5BYL Resolution: 2.35→89.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.228 / 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: 49.218 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 2.35→89.13 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi




X-RAY DIFFRACTION
Canada, 1items
Citation


















PDBj






