+Open data
-Basic information
Entry | Database: PDB / ID: 5w7r | |||||||||||||||||||||
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Title | Crystal structure of OxaC in complex with SAH and oxaline | |||||||||||||||||||||
Components | OxaC | |||||||||||||||||||||
Keywords | TRANSFERASE / methyltransferase / penicillium oxalicum / oxaline / indole alkaloid | |||||||||||||||||||||
Function / homology | Function and homology information : / : / O-methyltransferase activity / secondary metabolite biosynthetic process / methylation Similarity search - Function | |||||||||||||||||||||
Biological species | Penicillium oxalicum (fungus) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.497 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 | 5w7r.cif.gz | 95.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w7r.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w7r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w7r_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 5w7r_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5w7r_validation.xml.gz | 17.4 KB | Display | |
Data in CIF | 5w7r_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/5w7r ftp://data.pdbj.org/pub/pdb/validation_reports/w7/5w7r | HTTPS FTP |
-Related structure data
Related structure data | 5w7kC 5w7mC 5w7pSC 5w7sC 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-9Z7 / ( |
#3: Chemical | ChemComp-SAH / |
#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: 3.41 Å3/Da / Density % sol: 63.93 % |
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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: 2.4→46.494 Å / Num. obs: 23938 / % possible obs: 99.93 % / Redundancy: 16.4 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 19.96 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W7P Resolution: 2.497→46.494 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.18
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 150.19 Å2 / Biso mean: 70.4814 Å2 / Biso min: 30 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.497→46.494 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: 7 / % reflection obs: 100 %
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