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Yorodumi- PDB-2bue: Structure of AAC(6')-Ib in complex with Ribostamycin and Coenzyme A. -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bue | ||||||
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Title | Structure of AAC(6')-Ib in complex with Ribostamycin and Coenzyme A. | ||||||
Components | AAC(6')-IB | ||||||
Keywords | TRANSFERASE / GNAT / AMINOGLYCOSIDE / FLUOROQUINOLONE / ACETYLTRANSFERASE / ANTIBIOTIC RESISTANCE | ||||||
Function / homology | Function and homology information N-acyltransferase activity / nucleotidyltransferase activity / response to antibiotic / metal ion binding Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Vetting, M.W. / Park, C.H. / Hedge, S.S. / Hooper, D.C. / Blanchard, J.S. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Mechanistic and Structural Analysis of Aminoglycoside N-Acetyltransferase Aac(6')-Ib and its Bifunctional, Fluoroquinolone-Active Aac(6')-Ib-Cr Variant. Authors: Vetting, M.W. / Park, C.H. / Hegde, S.S. / Jacoby, G.A. / Hooper, D.C. / Blanchard, J.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bue.cif.gz | 61.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bue.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 2bue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bue_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2bue_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2bue_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 2bue_validation.cif.gz | 17.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bu/2bue ftp://data.pdbj.org/pub/pdb/validation_reports/bu/2bue | HTTPS FTP |
-Related structure data
Related structure data | 1v0cSC 2vqyC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 22385.031 Da / Num. of mol.: 1 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q6SJ71, aminoglycoside 6'-N-acetyltransferase | ||||||
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#2: Chemical | ChemComp-COA / | ||||||
#3: Chemical | ChemComp-RIO / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | GSH ON N-TERMINUS FROM CLEAVED HEXA-HISTIDINE TAG | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 55.4 % / Description: ISOMORPHOUS WITH PDB ENTRY 1V0C |
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Crystal grow | Method: vapor diffusion / pH: 6.75 Details: PROTEIN (10MG/ML, 20 MM TRIS PH 7.5, 20 MM NACL, 3 MM ACCOA) PRECIPITANT (20% PEG3350, 200 MM CALCIUM ACETATE, 100 MM NACACODYLATE PH 6.75) VAPOR DIFFUSION UNDER OIL |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 |
Detector | Type: RIGAKU-MSC RAXIS-IV / Detector: IMAGE PLATE / Date: Oct 18, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→24.29 Å / Num. obs: 27341 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 33.2 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 6.9 / % possible all: 84.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1V0C Resolution: 1.7→149.07 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.663 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.097 / 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: 17.58 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→149.07 Å
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Refine LS restraints |
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