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Yorodumi- PDB-6ecd: Vlm2 thioesterase domain with genetically encoded 2,3-diaminoprop... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ecd | ||||||
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Title | Vlm2 thioesterase domain with genetically encoded 2,3-diaminopropionic acid bound with a tetradepsipeptide | ||||||
Components |
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Keywords | HYDROLASE / thioesterase / thioesterase domain / NRPS / non-ribosomal peptide synthetase / nonribosomal peptide synthetase / valinomycin / depsipeptide / unnatural amino acid / 2 / 3-diaminopropionic acid | ||||||
Function / homology | Function and homology information : / amino acid activation for nonribosomal peptide biosynthetic process / carboxylic acid metabolic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity / cytosol Similarity search - Function | ||||||
Biological species | Streptomyces tsusimaensis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Alonzo, D.A. / Huguenin-Dezot, N. / Heberlig, G.W. / Mahesh, M. / Nguyen, D.P. / Dornan, M.H. / Boddy, C.N. / Chin, J.W. / Schmeing, T.M. | ||||||
Funding support | Canada, 1items
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Citation | Journal: Nature / Year: 2019 Title: Trapping biosynthetic acyl-enzyme intermediates with encoded 2,3-diaminopropionic acid. Authors: Huguenin-Dezot, N. / Alonzo, D.A. / Heberlig, G.W. / Mahesh, M. / Nguyen, D.P. / Dornan, M.H. / Boddy, C.N. / Schmeing, T.M. / Chin, J.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ecd.cif.gz | 179.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ecd.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 6ecd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ecd_validation.pdf.gz | 432.9 KB | Display | wwPDB validaton report |
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Full document | 6ecd_full_validation.pdf.gz | 433.3 KB | Display | |
Data in XML | 6ecd_validation.xml.gz | 11.6 KB | Display | |
Data in CIF | 6ecd_validation.cif.gz | 16 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ec/6ecd ftp://data.pdbj.org/pub/pdb/validation_reports/ec/6ecd | HTTPS FTP |
-Related structure data
Related structure data | 6ecbSC 6eccC 6eceC 6ecfC 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 33095.512 Da / Num. of mol.: 1 / Fragment: thioesterase domain (UNP residues 2368-2655) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces tsusimaensis (bacteria) / Gene: vlm2 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q1PSF3, Hydrolases; Acting on ester bonds; Thioester hydrolases |
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#2: Protein/peptide | Mass: 388.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#3: 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: 4.42 Å3/Da / Density % sol: 72.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.65 M DL-malic acid, pH 8.0, 25 mM HEPES, pH 8.0, 100 mM sodium chloride, 0.2 mM TCEP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 13, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→107.69 Å / Num. obs: 48063 / % possible obs: 100 % / Redundancy: 37.2 % / Biso Wilson estimate: 37.63 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.02 / Rrim(I) all: 0.124 / Net I/σ(I): 23.3 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 3071 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 6ECB Resolution: 1.9→107.69 Å / SU ML: 0.1974 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.7972
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 59.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→107.69 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 351.708539507 Å / Origin y: 132.478698021 Å / Origin z: 381.98961583 Å
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Refinement TLS group | Selection details: all |