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Yorodumi- PDB-6erd: Crystal structure of a putative acetyltransferase from Bacillus c... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 6erd | ||||||
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| Title | Crystal structure of a putative acetyltransferase from Bacillus cereus species. | ||||||
Components | (Aminoglycoside N6'-acetyltransferase) x 2 | ||||||
Keywords | TRANSFERASE / Acetyltransferase Bacillus cereus Unidentified acetyl acceptor | ||||||
| Function / homology | aminoglycoside 6'-N-acetyltransferase activity / aminoglycoside 6'-N-acetyltransferase / Acetyltransferase (GNAT) domain / N-acetyltransferase activity / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / metal ion binding / Aminoglycoside N6'-acetyltransferase Function and homology information | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Silvestre, H.L. / Bolanos-Garcia, V.M. / Asensio, J.L. / Blundell, T.L. / Bastida, A. | ||||||
Citation | Journal: Int.J.Biol.Macromol. / Year: 2024Title: 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: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 6erd.cif.gz | 304.1 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb6erd.ent.gz | 248.6 KB | Display | PDB format |
| PDBx/mmJSON format | 6erd.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 6erd_validation.pdf.gz | 491 KB | Display | wwPDB validaton report |
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| Full document | 6erd_full_validation.pdf.gz | 498.8 KB | Display | |
| Data in XML | 6erd_validation.xml.gz | 33.3 KB | Display | |
| Data in CIF | 6erd_validation.cif.gz | 47.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/er/6erd ftp://data.pdbj.org/pub/pdb/validation_reports/er/6erd | HTTPS FTP |
-Related structure data
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Links
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Assembly
| Deposited unit | ![]()
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| 1 | ![]()
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| 2 | ![]()
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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
| #1: Protein | Mass: 24577.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: BC_2494 / Production host: ![]() References: UniProt: Q81D84, aminoglycoside 6'-N-acetyltransferase #2: Protein | Mass: 24501.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711 Gene: BC_2494 / Production host: ![]() References: UniProt: Q81D84, aminoglycoside 6'-N-acetyltransferase #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.11 Å3/Da / Density % sol: 41.83 % |
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| Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 30%PEG 6000 100mM Hepes pH7.0 1M LiCl 10 mM BME |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
| Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 7, 2010 |
| Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
| Reflection | Resolution: 1.92→83.97 Å / Num. obs: 60997 / % possible obs: 100 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.053 / Rrim(I) all: 0.104 / Net I/σ(I): 15.5 |
| Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.9 / Num. unique all: 4505 / Rpim(I) all: 0.425 / Rrim(I) all: 0.834 / % possible all: 100 |
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Processing
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| Refinement | Method to determine structure: MAD / Resolution: 2→44.97 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 7.354 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.141 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Displacement parameters | Biso mean: 28.07 Å2
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| Refinement step | Cycle: 1 / Resolution: 2→44.97 Å
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