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Yorodumi- PDB-8g3j: Non-ribosomal PCP-C didomain R2577G (thioether stabilised glycoli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8g3j | |||||||||
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Title | Non-ribosomal PCP-C didomain R2577G (thioether stabilised glycolic acid) acceptor bound state | |||||||||
Components | PCP-C didomain | |||||||||
Keywords | BIOSYNTHETIC PROTEIN / NRPS / C-domain / PCP-domain | |||||||||
Function / homology | Function and homology information amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity / cytosol Similarity search - Function | |||||||||
Biological species | Thermobifida fusca YX (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | |||||||||
Authors | Ho, Y.T.C. / Izore, T. / Cryle, M.J. | |||||||||
Funding support | Australia, 2items
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Citation | Journal: Front Catal / Year: 2023 Title: Exploring the selectivity and engineering potential of an NRPS condensation domain involved in the biosynthesis of the thermophilic siderophore fuscachelin Authors: Ho, Y.T.C. / Izore, T. / Kaczmarski, J.A. / Marschall, E. / Ratnayake, M. / Tailhades, J. / Steer, D.L. / Schittenhelm, R.B. / Tosin, M. / 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 | 8g3j.cif.gz | 215.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8g3j.ent.gz | 169 KB | Display | PDB format |
PDBx/mmJSON format | 8g3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/8g3j ftp://data.pdbj.org/pub/pdb/validation_reports/g3/8g3j | HTTPS FTP |
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-Related structure data
Related structure data | 8g3iC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 57387.809 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca YX (bacteria) / Strain: YX / Gene: Tfu_1867 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q47NR9 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.66 Å3/Da / Density % sol: 53.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: PEG 3350, Magnesium formate |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 25, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95372 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→47.2 Å / Num. obs: 69783 / % possible obs: 98 % / Redundancy: 2 % / CC1/2: 0.842 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.1→2.175 Å / Num. unique obs: 6859 / CC1/2: 0.432 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→47.2 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.06 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→47.2 Å
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Refine LS restraints |
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LS refinement shell |
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