+Open data
-Basic information
Entry | Database: PDB / ID: 6bc3 | ||||||
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Title | Cryo X-ray structure of sisomicin bound AAC-VIa | ||||||
Components | AAC 3-VI protein | ||||||
Keywords | TRANSFERASE/ANTIBIOTIC / acetyltransferase / TRANSFERASE-ANTIBIOTIC complex | ||||||
Function / homology | Function and homology information aminoglycoside 3-N-acetyltransferase / aminoglycoside 3-N-acetyltransferase activity / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | Enterobacter cloacae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.047 Å | ||||||
Authors | Cuneo, M.J. / Kumar, P. / Serpersu, E.H. | ||||||
Citation | Journal: Sci Adv / Year: 2018 Title: A low-barrier hydrogen bond mediates antibiotic resistance in a noncanonical catalytic triad. Authors: Kumar, P. / Serpersu, E.H. / Cuneo, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6bc3.cif.gz | 73.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6bc3.ent.gz | 51.2 KB | Display | PDB format |
PDBx/mmJSON format | 6bc3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6bc3_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6bc3_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6bc3_validation.xml.gz | 14.3 KB | Display | |
Data in CIF | 6bc3_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/6bc3 ftp://data.pdbj.org/pub/pdb/validation_reports/bc/6bc3 | HTTPS FTP |
-Related structure data
Related structure data | 6bbrC 6bbzC 6bc2C 6bc4C 6bc5C 6bc6SC 6bc7C 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: 32344.461 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: aac 3-VI / Production host: Escherichia coli (E. coli) / References: UniProt: Q47030 |
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#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-SIS / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.34 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.1 M sodium citrate, pH 5.6, 0.2 M ammonium acetate, 10% glycerol, 17-25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 14, 2017 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.047→50 Å / Num. obs: 18004 / % possible obs: 99.3 % / Redundancy: 2.9 % / Biso Wilson estimate: 31.58 Å2 / Rmerge(I) obs: 0.1 / Χ2: 1.38 / Net I/σ(I): 10.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6BC6 Resolution: 2.047→38.767 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.01 / 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: 2.047→38.767 Å
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Refine LS restraints |
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LS refinement shell |
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