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Yorodumi- PDB-2cnm: RimI - Ribosomal S18 N-alpha-protein acetyltransferase in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2cnm | ||||||
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Title | RimI - Ribosomal S18 N-alpha-protein acetyltransferase in complex with a bisubstrate inhibitor (Cterm-Arg-Arg-Phe-Tyr-Arg-Ala-N-alpha- acetyl-S-CoA). | ||||||
Components |
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Keywords | TRANSFERASE / N-ALPHA ACETYLATION / GCN5-N-ACETYLTRANSFERASE / RIBOSOMAL PROTEIN / ACETYLTRANSFERASE / GNAT / ACYLTRANSFERASE | ||||||
Function / homology | Function and homology information [ribosomal protein bS18]-alanine N-acetyltransferase / peptide-alanine-alpha-N-acetyltransferase activity / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / structural constituent of ribosome / translation / cytoplasm Similarity search - Function | ||||||
Biological species | SALMONELLA TYPHIMURIUM LT2 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SIRAS / Resolution: 2.6 Å | ||||||
Authors | Vetting, M.W. / Yu, M. / Bareich, D.C. / Blanchard, J.S. | ||||||
Citation | Journal: Protein Sci. / Year: 2008 Title: Crystal Structure of Rimi from Salmonella Typhimurium Lt2, the Gnat Responsible for N{Alpha}- Acetylation of Ribosomal Protein S18. Authors: Vetting, M.W. / Bareich, D.C. / Yu, M. / 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 | 2cnm.cif.gz | 105.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cnm.ent.gz | 88.7 KB | Display | PDB format |
PDBx/mmJSON format | 2cnm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/2cnm ftp://data.pdbj.org/pub/pdb/validation_reports/cn/2cnm | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | THE PROTEIN IS A MONOMER IS SOLUTION. THE TRIMER/HEXAMER OBSERVED IN THE ASU IS NON- PHYSIOLOGICAL AND IS AN ARTEFACT OF CRYSTAL PACKING. |
-Components
#1: Protein | Mass: 18325.762 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SALMONELLA TYPHIMURIUM LT2 (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: Q8ZJW4, ribosomal-protein-alanine N-acetyltransferase #2: Protein/peptide | Mass: 897.060 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) SALMONELLA TYPHIMURIUM LT2 (bacteria) / References: UniProt: V2H9S5, UniProt: Q8ZK81*PLUS #3: Chemical | ChemComp-COA / #4: Water | ChemComp-HOH / | Compound details | BIOMOLECUL | |
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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: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | pH: 5.5 Details: 15% PEG400 (W/V), 100 MM NACITRATE PH 5.5, 100 MM (NH4)2SO4 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200B / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH RAXIS IV / Detector: IMAGE PLATE / Details: OSMIC CONFOCAL MAXFLUX OPTICS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→40 Å / Num. obs: 19233 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.4 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: SIRAS / Resolution: 2.6→98.53 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 20.305 / SU ML: 0.208 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.571 / ESU R Free: 0.311 / 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: 28.56 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→98.53 Å
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