+Open data
-Basic information
Entry | Database: PDB / ID: 5xoh | ||||||
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Title | Crystal structure of bergaptol o-methyltransferase complex | ||||||
Components | Bergaptol O-methyltransferase | ||||||
Keywords | TRANSFERASE / bergaptol o-methyltransferase | ||||||
Function / homology | Function and homology information 5-hydroxyfuranocoumarin 5-O-methyltransferase activity / 5-hydroxyfuranocoumarin 5-O-methyltransferase / coumarin biosynthetic process / response to jasmonic acid / S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity / cytoplasm Similarity search - Function | ||||||
Biological species | Peucedanum praeruptorum (bai hua qian hu) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å | ||||||
Authors | Zhou, Y. / Zeng, Z. | ||||||
Citation | Journal: To Be Published Title: Crystal structure of bergaptol o-methyltransferase complex Authors: Zhou, Y. / Zeng, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xoh.cif.gz | 149.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xoh.ent.gz | 117.9 KB | Display | PDB format |
PDBx/mmJSON format | 5xoh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5xoh_validation.pdf.gz | 743.1 KB | Display | wwPDB validaton report |
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Full document | 5xoh_full_validation.pdf.gz | 750.3 KB | Display | |
Data in XML | 5xoh_validation.xml.gz | 15.9 KB | Display | |
Data in CIF | 5xoh_validation.cif.gz | 21.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xo/5xoh ftp://data.pdbj.org/pub/pdb/validation_reports/xo/5xoh | HTTPS FTP |
-Related structure data
Similar structure data |
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-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: 39310.207 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peucedanum praeruptorum (bai hua qian hu) Gene: BMT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: A0A166U5H3, 5-hydroxyfuranocoumarin 5-O-methyltransferase |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-8B6 / |
#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: 2.24 Å3/Da / Density % sol: 45.03 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 40% PEG300, Cacodylate pH6.5 and 200mM Calcium acetate The crystals were flash-frozen in liquid nitrogen and cryoprotected by adding glycerol to a final concentration of 20%. |
-Data collection
Diffraction | Mean temperature: 273 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å |
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: CCD / Date: Dec 25, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97846 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 18833 / % possible obs: 99.8 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.134 / Net I/σ(I): 29.8 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 2.07 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→33.06 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→33.06 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: 49.7208 Å / Origin y: 11.9347 Å / Origin z: 79.7936 Å
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Refinement TLS group | Selection details: ALL |