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Yorodumi- PDB-6ch4: Aminoglycoside Phosphotransferase (2'')-Ia S376N mutant in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ch4 | ||||||
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Title | Aminoglycoside Phosphotransferase (2'')-Ia S376N mutant in complex with GMPPNP and Magnesium | ||||||
Components | Bifunctional AAC/APH | ||||||
Keywords | TRANSFERASE / Kinase / Antibiotic / Aminoglycoside / Resistance / TRANSFERASE-Antibiotic complex | ||||||
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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Caldwell, S.J. / Berghuis, A.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Antimicrob. Agents Chemother. / Year: 2018 Title: Plasticity of Aminoglycoside Binding to Antibiotic Kinase APH(2′′)-Ia. Authors: Caldwell, S.J. / 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 | 6ch4.cif.gz | 517.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ch4.ent.gz | 424.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ch4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ch4_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6ch4_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 6ch4_validation.xml.gz | 50.9 KB | Display | |
Data in CIF | 6ch4_validation.cif.gz | 70.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ch/6ch4 ftp://data.pdbj.org/pub/pdb/validation_reports/ch/6ch4 | HTTPS FTP |
-Related structure data
Related structure data | 6c5uC 6cavC 6ceyC 6cgdC 6cggC 5iqaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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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: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 35975.223 Da / Num. of mol.: 4 / Mutation: S376N Source method: isolated from a genetically manipulated source Details: C-terminal domain of AAC(6')-Ie/APH(2'')-Ia bifunctional enzyme, residues 175-479. Mutant S376N 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, aminoglycoside 2''-phosphotransferase #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: 2.87 Å3/Da / Density % sol: 56.44 % |
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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: 2.3→58.89 Å / Num. obs: 71190 / % possible obs: 100 % / Redundancy: 4.3 % / Biso Wilson estimate: 44.012 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.104 / Rrim(I) all: 0.155 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.965 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4576 / CC1/2: 0.434 / Rpim(I) all: 0.741 / Rrim(I) all: 1.11 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB 5IQA Resolution: 2.3→58.89 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 12.76 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.192 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 51.437 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→58.89 Å
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Refine LS restraints |
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