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Yorodumi- PDB-1s7l: RimL- Ribosomal L7/L12 alpha-N-protein acetyltransferase in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1s7l | ||||||
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Title | RimL- Ribosomal L7/L12 alpha-N-protein acetyltransferase in complex with Coenzyme A (CoA-Cys134 Disulfide) | ||||||
Components | acetyl transferase | ||||||
Keywords | TRANSFERASE / acetyltransferase / GNAT / alpha-N-protein acetyltransferase / Coenzyme A / L7/L12 | ||||||
Function / homology | Function and homology information peptide-alanine-alpha-N-acetyltransferase activity / peptide-serine-alpha-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm Similarity search - Function | ||||||
Biological species | Salmonella typhimurium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Vetting, M.W. / de Carvalho, L.P. / Roderick, S.L. / Blanchard, J.S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: A novel dimeric structure of the RimL Nalpha-acetyltransferase from Salmonella typhimurium. Authors: Vetting, M.W. / de Carvalho, L.P. / Roderick, S.L. / 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 | 1s7l.cif.gz | 53.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1s7l.ent.gz | 36.6 KB | Display | PDB format |
PDBx/mmJSON format | 1s7l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s7/1s7l ftp://data.pdbj.org/pub/pdb/validation_reports/s7/1s7l | HTTPS FTP |
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-Related structure data
Related structure data | 1s7fSC 1s7kC 1s7nC S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by the operations y, x, -z |
-Components
#1: Protein | Mass: 20912.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: RimL / Plasmid: pet28a+ / Production host: Escherichia coli (E. coli) References: UniProt: Q8ZPC0, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-COA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion under oil / pH: 8 Details: pentaerythritiol ethoxylate 797, triethanolamine, ammonium sulfate, acetylcoenzyme A, DTT, pH 8, vapor diffusion under oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 3, 2003 / Details: MSC Blue Confocal |
Radiation | Monochromator: MSC Blue Confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 10924 / Num. obs: 10924 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 40.3 Å2 / Rsym value: 0.04 / Net I/σ(I): 20.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3.9 % / Rsym value: 0.165 / % possible all: 93.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB Entry 1S7F Resolution: 2.3→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.38 Å / Rfactor Rfree: 0.265 / Rfactor Rwork: 0.239 |