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Yorodumi- PDB-1jmk: Structural Basis for the Cyclization of the Lipopeptide Antibioti... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jmk | ||||||
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Title | Structural Basis for the Cyclization of the Lipopeptide Antibiotic Surfactin by the Thioesterase Domain SrfTE | ||||||
Components | Surfactin Synthetase | ||||||
Keywords | HYDROLASE / Thioesterase / Non-ribosomal Peptide Synthesis / Alpha-beta Hydrolase / Cyclic Peptide | ||||||
Function / homology | Function and homology information amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / sporulation resulting in formation of a cellular spore / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.71 Å | ||||||
Authors | Bruner, S.D. / Weber, T. / Kohli, R.M. / Schwarzer, D. / Marahiel, M.A. / Walsh, C.T. / Stubbs, M.T. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain SrfTE. Authors: Bruner, S.D. / Weber, T. / Kohli, R.M. / Schwarzer, D. / Marahiel, M.A. / Walsh, C.T. / Stubbs, M.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jmk.cif.gz | 102.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jmk.ent.gz | 80.1 KB | Display | PDB format |
PDBx/mmJSON format | 1jmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jm/1jmk ftp://data.pdbj.org/pub/pdb/validation_reports/jm/1jmk | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 25692.805 Da / Num. of mol.: 2 / Fragment: Thioesterase Domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: SrfA-C / Plasmid: pQE60 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q08787 #2: Chemical | #3: Water | ChemComp-HOH / | |
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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: 2.8 Å3/Da / Density % sol: 56.1 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8M Ammonium Sulfate, 0.1M HEPES 7.5, 2% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Monochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.71→25 Å / Num. all: 63148 / Num. obs: 62391 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 | ||||||||||||||||||
Reflection shell | Resolution: 1.71→1.77 Å / % possible all: 92.5 | ||||||||||||||||||
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 663308 / Rmerge(I) obs: 0.054 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 92.5 % / Num. unique obs: 5717 / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.71→25 Å / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.71→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.71→1.82 Å / Rfactor Rfree error: 0.011
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Refinement | *PLUS Lowest resolution: 25 Å / % reflection Rfree: 10 % / Rfactor obs: 0.222 / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.23 | |||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.322 / Rfactor Rwork: 0.308 / Rfactor obs: 0.308 |