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Yorodumi- PDB-5iqh: 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: 5iqh | ||||||
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| Title | Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH(2'')-Ia) S214A 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 /  SYNCHROTRON /  FOURIER SYNTHESIS / Resolution: 2.25 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 |  5iqh.cif.gz | 526.1 KB | Display |  PDBx/mmCIF format | 
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| PDB format |  pdb5iqh.ent.gz | 431.7 KB | Display |  PDB format | 
| PDBx/mmJSON format |  5iqh.json.gz | Tree view |  PDBx/mmJSON format | |
| Others |  Other downloads | 
-Validation report
| Summary document |  5iqh_validation.pdf.gz | 1.6 MB | Display |  wwPDB validaton report | 
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| Full document |  5iqh_full_validation.pdf.gz | 1.6 MB | Display | |
| Data in XML |  5iqh_validation.xml.gz | 54.6 KB | Display | |
| Data in CIF |  5iqh_validation.cif.gz | 78.4 KB | Display | |
| Arichive directory |  https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqh ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqh | HTTPS FTP  | 
-Related structure data
| Related structure data | ![]() 5bylSC ![]() 5iqaC ![]() 5iqbC ![]() 5iqcC ![]() 5iqdC ![]() 5iqeC ![]() 5iqfC ![]() 5iqgC ![]() 5iqiC 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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| Unit cell | 
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| Noncrystallographic symmetry (NCS) | NCS domain: 
 NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: _ 
 NCS ensembles : 
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Components
-Protein , 1 types, 4 molecules ABCD   
| #1: Protein | Mass: 35932.199 Da / Num. of mol.: 4 / Fragment: C-terminal domain (UNP residues 175-479) / Mutation: S214A Source method: isolated from a genetically manipulated source Details: C-terminal domain of AAC(6')-Ie/APH(2'')-Ia bifunctional enzyme, residues 175-479. S214a Mutant 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  | 
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-Non-polymers , 5 types, 986 molecules 








| #2: Chemical | ChemComp-GNP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | #6: 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: 2.82 Å3/Da / Density % sol: 56.32 % | 
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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:  SYNCHROTRON / Site:  CLSI   / Beamline: 08ID-1 / Wavelength: 0.9795 Å | 
| Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 25, 2014 | 
| Radiation | Monochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray  | 
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | 
| Reflection | Resolution: 2.25→89.99 Å / Num. obs: 75692 / % possible obs: 96.6 % / Redundancy: 2 % / Biso Wilson estimate: 42.2 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10.6 | 
| Reflection shell | Resolution: 2.25→2.3 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 2.4 / % possible all: 98.3 | 
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Processing
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| Refinement | Method to determine structure:  FOURIER SYNTHESISStarting model: 5BYL Resolution: 2.25→89.99 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.952 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.182 / 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: 48.856 Å2
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| Refinement step | Cycle: LAST / Resolution: 2.25→89.99 Å
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| Refine LS restraints | 
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