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Yorodumi- PDB-5iqi: Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 5iqi | ||||||
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| Title | Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) Y237F mutant in complex with GMPPNP 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: 2.15 Å | ||||||
Authors | Caldwell, S.J. / Berghuis, A.M. | ||||||
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 |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 5iqi.cif.gz | 539.7 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb5iqi.ent.gz | 443 KB | Display | PDB format |
| PDBx/mmJSON format | 5iqi.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 5iqi_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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| Full document | 5iqi_full_validation.pdf.gz | 1.6 MB | Display | |
| Data in XML | 5iqi_validation.xml.gz | 60.1 KB | Display | |
| Data in CIF | 5iqi_validation.cif.gz | 88.5 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqi ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqi | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 5bylSC ![]() 5iqaC ![]() 5iqbC ![]() 5iqcC ![]() 5iqdC ![]() 5iqeC ![]() 5iqfC ![]() 5iqgC ![]() 5iqhC S: Starting model for refinement C: citing same article ( |
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| Similar structure data |
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Links
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Assembly
| Deposited unit | ![]()
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| 2 | ![]()
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| 3 | ![]()
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| 4 | ![]()
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| Unit cell |
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| Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _
NCS ensembles :
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Components
| #1: Protein | Mass: 35932.199 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 175-479) / Mutation: Y237F Source method: isolated from a genetically manipulated source Details: C-terminal domain of AAC(6')-Ie/APH(2'')-Ia bifunctional enzyme, residues 175-479 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 #2: Chemical | ChemComp-GNP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Water | ChemComp-HOH / | |
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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: 2.81 Å3/Da / Density % sol: 56.2 % |
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| 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 |
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| Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å |
| Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 4, 2016 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
| Reflection | Resolution: 2.15→89.76 Å / Num. obs: 86424 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 34.2 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.082 / Net I/σ(I): 8.4 |
| Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 1.6 / % possible all: 97.2 |
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Processing
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| Refinement | Method to determine structure: FOURIER SYNTHESISStarting model: 5BYL Resolution: 2.15→89.76 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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| 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: 46.623 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.15→89.76 Å
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| Refine LS restraints |
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