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Yorodumi- PDB-5w7s: Crystal structure of OxaC in complex with sinefungin and meleagrin -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w7s | |||||||||||||||||||||
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Title | Crystal structure of OxaC in complex with sinefungin and meleagrin | |||||||||||||||||||||
Components | OxaC | |||||||||||||||||||||
Keywords | TRANSFERASE / methyltransferase / penicillium oxalicum / oxaline / indole alkaloid | |||||||||||||||||||||
Function / homology | Function and homology information secondary metabolite biosynthetic process / O-methyltransferase activity / methylation Similarity search - Function | |||||||||||||||||||||
Biological species | Penicillium oxalicum (fungus) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.948 Å | |||||||||||||||||||||
Authors | Newmister, S.A. / Romminger, S. / Schmidt, J.J. / Williams, R.M. / Smith, J.L. / Berlinck, R.G.S. / Sherman, D.H. | |||||||||||||||||||||
Funding support | United States, Brazil, 6items
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Citation | Journal: Org. Biomol. Chem. / Year: 2018 Title: Unveiling sequential late-stage methyltransferase reactions in the meleagrin/oxaline biosynthetic pathway. Authors: Newmister, S.A. / Romminger, S. / Schmidt, J.J. / Williams, R.M. / Smith, J.L. / Berlinck, R.G.S. / Sherman, D.H. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w7s.cif.gz | 173.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w7s.ent.gz | 134.3 KB | Display | PDB format |
PDBx/mmJSON format | 5w7s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/5w7s ftp://data.pdbj.org/pub/pdb/validation_reports/w7/5w7s | HTTPS FTP |
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-Related structure data
Related structure data | 5w7kC 5w7mC 5w7pSC 5w7rC 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: 47284.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Penicillium oxalicum (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B2TT09 |
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#2: Chemical | ChemComp-9Z1 / ( |
#3: Chemical | ChemComp-SFG / |
#4: 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: 3.46 Å3/Da / Density % sol: 64.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.6 Details: lithium sulfate, ammonium sulfate, sodium citrate, glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.948→46.685 Å / Num. obs: 15374 / % possible obs: 99.77 % / Redundancy: 14.7 % / Net I/σ(I): 14.25 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W7P Resolution: 2.948→46.685 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 183.77 Å2 / Biso mean: 83.0927 Å2 / Biso min: 26.62 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.948→46.685 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Origin x: 20.7285 Å / Origin y: 131.9851 Å / Origin z: 29.9758 Å
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Refinement TLS group |
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