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Yorodumi- PDB-7wew: Structure of adenylation domain of epsilon-poly-L-lysine synthase -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wew | ||||||||||||
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Title | Structure of adenylation domain of epsilon-poly-L-lysine synthase | ||||||||||||
Components | Epsilon-poly-L-lysine synthase | ||||||||||||
Keywords | LIGASE / adenylation-domain / NRPS | ||||||||||||
Function / homology | Function and homology information phosphopantetheine binding / transferase activity / membrane => GO:0016020 Similarity search - Function | ||||||||||||
Biological species | Streptomyces albulus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | Okamoto, T. / Yamanaka, K. / Hamano, Y. / Nagano, S. / Hino, T. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2022 Title: Crystal structure of the adenylation domain from an epsilon-poly-l-lysine synthetase provides molecular mechanism for substrate specificity Authors: Okamoto, T. / Yamanaka, K. / Hamano, Y. / Nagano, S. / Hino, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wew.cif.gz | 123.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wew.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 7wew.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/7wew ftp://data.pdbj.org/pub/pdb/validation_reports/we/7wew | HTTPS FTP |
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-Related structure data
Related structure data | 3vnqS S: Starting model for refinement |
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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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 53721.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces albulus (bacteria) / Gene: pls / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: B5BR95 | ||||||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Chemical | ChemComp-LAD / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3 Å3/Da / Density % sol: 59.37 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2 M potassium sodium tartrate 0.1 M trisodium citrate 1.8 M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jan 22, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→45.28 Å / Num. obs: 28719 / % possible obs: 99.61 % / Redundancy: 8.2 % / Biso Wilson estimate: 39.04 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.224 / Rpim(I) all: 0.083 / Rrim(I) all: 0.239 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 8 % / Rmerge(I) obs: 1.275 / Num. unique obs: 2791 / CC1/2: 0.741 / Rpim(I) all: 0.481 / Rrim(I) all: 1.366 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VNQ Resolution: 2.3→45.28 Å / SU ML: 0.3079 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.4718 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.34 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→45.28 Å
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Refine LS restraints |
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LS refinement shell |
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