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Yorodumi- PDB-8q6u: Crystal structure of a double mutant acetyltransferase from Bacil... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q6u | ||||||
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Title | Crystal structure of a double mutant acetyltransferase from Bacillus cereus species. | ||||||
Components | Aminoglycoside N6'-acetyltransferase | ||||||
Keywords | TRANSFERASE / Acetyltransferase | ||||||
Function / homology | aminoglycoside 6'-N-acetyltransferase / aminoglycoside 6'-N-acetyltransferase activity / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminoglycoside N6'-acetyltransferase Function and homology information | ||||||
Biological species | Bacillus cereus ATCC 14579 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.516 Å | ||||||
Authors | Silvestre, H.L. | ||||||
Funding support | Spain, 1items
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Citation | Journal: Int.J.Biol.Macromol. / Year: 2024 Title: Functional and structural characterisation of RimL from Bacillus cereus, a new N alpha-acetyltransferase of ribosomal proteins that was wrongly assigned as an aminoglycosyltransferase. Authors: Leonardo Silvestre, H. / Asensio, J.L. / Blundell, T.L. / Bastida, A. / Bolanos-Garcia, V.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q6u.cif.gz | 154.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q6u.ent.gz | 121 KB | Display | PDB format |
PDBx/mmJSON format | 8q6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/8q6u ftp://data.pdbj.org/pub/pdb/validation_reports/q6/8q6u | HTTPS FTP |
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-Related structure data
Related structure data | 6erdC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 19667.611 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_2494 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q81D84 #2: Chemical | ChemComp-EDO / #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: 2.3 Å3/Da / Density % sol: 46.5 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, sitting drop Details: 2mM zinc chloride, 100 mM Tris pH 8.0, 20 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2010 |
Radiation | Monochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.516→52.321 Å / Num. obs: 31633 / % possible obs: 74.5 % / Redundancy: 6.3 % / CC1/2: 0.999 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.516→1.636 Å / Num. unique obs: 1583 / CC1/2: 0.693 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.516→19.32 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.14 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.123
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Displacement parameters | Biso mean: 22.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.516→19.32 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.52→1.59 Å
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Refinement TLS params. | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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