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Yorodumi- PDB-6dyo: C-terminal condensation domain of Ebony in complex with L-Dopamine -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dyo | ||||||
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Title | C-terminal condensation domain of Ebony in complex with L-Dopamine | ||||||
Components | Ebony | ||||||
Keywords | BIOSYNTHETIC PROTEIN / NRPS / Condensation domain / Peptide-bond formation | ||||||
Function / homology | Function and homology information ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain Similarity search - Domain/homology | ||||||
Biological species | Drosophila melanogaster (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Izore, T. / Tailhades, J. / Hansen, M.H. / Kaczmarski, J.A. / Jackson, C.J. / Cryle, M.J. | ||||||
Funding support | Australia, 1items
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Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019 Title: Drosophila melanogasternonribosomal peptide synthetase Ebony encodes an atypical condensation domain. Authors: Izore, T. / Tailhades, J. / Hansen, M.H. / Kaczmarski, J.A. / Jackson, C.J. / Cryle, M.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dyo.cif.gz | 70 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dyo.ent.gz | 40.2 KB | Display | PDB format |
PDBx/mmJSON format | 6dyo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/6dyo ftp://data.pdbj.org/pub/pdb/validation_reports/dy/6dyo | HTTPS FTP |
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-Related structure data
Related structure data | 6dymSC 6dynC 6dyrC 6dysC 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
#1: Protein | Mass: 25991.506 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4GK78 |
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#2: Chemical | ChemComp-LDP / |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 400, HEPES, CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→46.07 Å / Num. obs: 5590 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.12 Å2 / Net I/σ(I): 6.1 |
Reflection shell | Resolution: 2.84→2.99 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6DYM Resolution: 2.84→46.07 Å / SU ML: 0.423 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2221
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.74 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→46.07 Å
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Refine LS restraints |
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LS refinement shell |
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