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- 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. | ||||||
![]() | (Aminoglycoside N6'-acetyltransferase) x 2 | ||||||
![]() | TRANSFERASE / Acetyltransferase Bacillus cereus Unidentified acetyl acceptor | ||||||
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 / metal ion binding / Aminoglycoside N6'-acetyltransferase![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Silvestre, H.L. / Bolanos-Garcia, V.M. / Asensio, J.L. / Blundell, T.L. / Bastida, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 304.1 KB | Display | ![]() |
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PDB format | ![]() | 248.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-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: ![]() |
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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: ![]() ![]() ![]() |
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: ![]()
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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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Refine LS restraints |
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