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Yorodumi- PDB-7csj: Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smeg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7csj | ||||||
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Title | Aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis-Complex with Coenzyme A and Gentamicin | ||||||
Components | Aminoglycoside 2'-N-acetyltransferase | ||||||
Keywords | TRANSFERASE / aminoglycoside acetyltransferase / antibiotics / gentamicin | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / response to antibiotic Similarity search - Function | ||||||
Biological species | Mycolicibacterium smegmatis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.168 Å | ||||||
Authors | Jeong, C.S. / Hwang, J. / Do, H. / Lee, J.H. | ||||||
Citation | Journal: Sci Rep / Year: 2020 Title: Structural and biochemical analyses of an aminoglycoside 2'-N-acetyltransferase from Mycolicibacterium smegmatis. Authors: Jeong, C.S. / Hwang, J. / Do, H. / Cha, S.S. / Oh, T.J. / Kim, H.J. / Park, H.H. / Lee, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7csj.cif.gz | 92.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7csj.ent.gz | 68.5 KB | Display | PDB format |
PDBx/mmJSON format | 7csj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/7csj ftp://data.pdbj.org/pub/pdb/validation_reports/cs/7csj | HTTPS FTP |
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-Related structure data
Related structure data | 7crmSC 7cs0C 7cs1C 7csiC 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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Unit cell |
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-Components
#1: Protein | Mass: 23198.838 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Gene: aac, MSMEG_0434, MSMEI_0423 / Production host: Escherichia coli (E. coli) References: UniProt: P94968, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-51G / | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.07 Å3/Da / Density % sol: 40.51 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.1M sodium citrate: citric acid (pH 5.5), 20% (w/v) PEG 3000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.168→50 Å / Num. obs: 20679 / % possible obs: 97.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 37.985 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 4.46 / Num. unique obs: 791 / % possible all: 76.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7CRM Resolution: 2.168→41.95 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.28 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.168→41.95 Å
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Refine LS restraints |
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LS refinement shell |
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