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Yorodumi- PDB-5iqi: Aminoglycoside Phosphotransferase (2'')-Ia (CTD of AAC(6')-Ie/APH... -
+Open data
-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 information aminoglycoside phosphotransferase activity / aminoglycoside 2''-phosphotransferase / N-acyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.15 Å | ||||||
Authors | Caldwell, S.J. / Berghuis, A.M. | ||||||
Citation | Journal: Structure / Year: 2016 Title: 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: MolmilJmol/JSmol |
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-Downloads & links
-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
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iq/5iqi ftp://data.pdbj.org/pub/pdb/validation_reports/iq/5iqi | HTTPS FTP |
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-Related structure data
Related structure data | 5bylSC 5iqaC 5iqbC 5iqcC 5iqdC 5iqeC 5iqfC 5iqgC 5iqhC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Staphylococcus aureus (bacteria) / Gene: aacA-aphD, R015, VRA0030 / Plasmid: pET-22b-APH(2'')-Ia / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(LDE3) 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 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting 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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