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Yorodumi- PDB-6cey: Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cey | ||||||
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Title | Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Lividomycin moieties | ||||||
Components | Bifunctional AAC/APH | ||||||
Keywords | TRANSFERASE/Antibiotic / Kinase / Antibiotic / Aminoglycoside / Resistance / Transferase / 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: 2.4 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 | 6cey.cif.gz | 521.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cey.ent.gz | 428.3 KB | Display | PDB format |
PDBx/mmJSON format | 6cey.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/6cey ftp://data.pdbj.org/pub/pdb/validation_reports/ce/6cey | HTTPS FTP |
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-Related structure data
Related structure data | 6c5uC 6cavC 6cgdC 6cggC 6ch4C 5iqaS 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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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: _ / Refine code: _
NCS ensembles :
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 35948.199 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source 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 |
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-Non-polymers , 5 types, 558 molecules
#2: Chemical | ChemComp-GNP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-LIV / ( | #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: 2.87 Å3/Da / Density % sol: 56.91 % |
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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: Nov 26, 2013 |
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: 2.4→90.73 Å / Num. obs: 63302 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 50.686 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.084 / Rrim(I) all: 0.127 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.4→2.46 Å / Redundancy: 4.2 % / Rmerge(I) obs: 1.345 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4441 / CC1/2: 0.287 / Rpim(I) all: 1.011 / Rrim(I) all: 1.538 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB 5IQA Resolution: 2.4→90.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.947 / SU B: 16.142 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: Author states that the ligand modelled is their best interpretation of the observed electron density with the tools available at deposition, but remains subject to some ambiguity in absolute ...Details: Author states that the ligand modelled is their best interpretation of the observed electron density with the tools available at deposition, but remains subject to some ambiguity in absolute configuration. The difference density was observed following the soaking of lividomycin to antibiotic-free crystals. Observed electron density likely reflects the superimposition of multiple weak binding modes, which would explain to low-level off-target activity of the enzyme as reported in studies of enzymatic regiospecificity.
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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: 59.493 Å2
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Refinement step | Cycle: 1 / Resolution: 2.4→90.73 Å
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Refine LS restraints |
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