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Yorodumi- PDB-6cav: Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cav | ||||||
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Title | Aminoglycoside Phosphotransferase (2'')-Ia in complex with GMPPNP, Magnesium, and Dibekacin | ||||||
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: 2.6 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 | 6cav.cif.gz | 516.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cav.ent.gz | 426 KB | Display | PDB format |
PDBx/mmJSON format | 6cav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cav_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6cav_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 6cav_validation.xml.gz | 50.1 KB | Display | |
Data in CIF | 6cav_validation.cif.gz | 68.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ca/6cav ftp://data.pdbj.org/pub/pdb/validation_reports/ca/6cav | HTTPS FTP |
-Related structure data
Related structure data | 6c5uC 6ceyC 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, 522 molecules
#2: Chemical | ChemComp-GNP / #3: Chemical | ChemComp-MG / #4: Chemical | #5: Chemical | ChemComp-84D / #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: 55.56 % |
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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: Aug 23, 2016 |
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: 2.6→98.34 Å / Num. obs: 48468 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 46.543 Å2 / CC1/2: 0.978 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.132 / Rrim(I) all: 0.194 / Net I/σ(I): 4.7 |
Reflection shell | Resolution: 2.6→2.68 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.072 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4406 / CC1/2: 0.358 / Rpim(I) all: 0.856 / Rrim(I) all: 1.273 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB 5IQA Resolution: 2.6→89.94 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.924 / SU B: 28.212 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 0.725 / ESU R Free: 0.304 / 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: 61.529 Å2
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Refinement step | Cycle: 1 / Resolution: 2.6→89.94 Å
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Refine LS restraints |
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