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Open data
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Basic information
Entry | Database: PDB / ID: 5xoh | ||||||
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Title | Crystal structure of bergaptol o-methyltransferase complex | ||||||
![]() | Bergaptol O-methyltransferase | ||||||
![]() | TRANSFERASE / bergaptol o-methyltransferase | ||||||
Function / homology | ![]() 5-hydroxyfuranocoumarin 5-O-methyltransferase / 5-hydroxyfuranocoumarin 5-O-methyltransferase activity / O-methyltransferase activity / methylation / protein dimerization activity Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhou, Y. / Zeng, Z. | ||||||
![]() | ![]() Title: Crystal structure of bergaptol o-methyltransferase complex Authors: Zhou, Y. / Zeng, Z. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 149.6 KB | Display | ![]() |
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PDB format | ![]() | 117.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 743.1 KB | Display | ![]() |
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Full document | ![]() | 750.3 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 21.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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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.) ![]() Gene: BMT / Production host: ![]() ![]() 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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 |