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- PDB-5xoh: Crystal structure of bergaptol o-methyltransferase complex -

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Basic information

Entry
Database: PDB / ID: 5xoh
TitleCrystal structure of bergaptol o-methyltransferase complex
ComponentsBergaptol O-methyltransferase
KeywordsTRANSFERASE / 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
Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily ...Plant methyltransferase dimerisation / O-methyltransferase dimerisation domain / O-methyltransferase domain / O-methyltransferase COMT-type / O-methyltransferase domain / SAM-dependent O-methyltransferase class II-type profile. / Vaccinia Virus protein VP39 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-oxidanylfuro[3,2-g]chromen-7-one / S-ADENOSYL-L-HOMOCYSTEINE / Bergaptol O-methyltransferase
Similarity search - Component
Biological speciesPeucedanum praeruptorum (bai hua qian hu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsZhou, Y. / Zeng, Z.
CitationJournal: To Be Published
Title: Crystal structure of bergaptol o-methyltransferase complex
Authors: Zhou, Y. / Zeng, Z.
History
DepositionMay 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bergaptol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8973
Polymers39,3101
Non-polymers5872
Water1,06359
1
A: Bergaptol O-methyltransferase
hetero molecules

A: Bergaptol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7946
Polymers78,6202
Non-polymers1,1734
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_646y+1,x-1,-z+11
Buried area8500 Å2
ΔGint-75 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.436, 59.436, 172.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

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Components

#1: Protein Bergaptol O-methyltransferase


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
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-8B6 / 4-oxidanylfuro[3,2-g]chromen-7-one


Mass: 202.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 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%.

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97846 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: CCD / Date: Dec 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97846 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX1.11_2567refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod 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
RfactorNum. reflection% reflection
Rfree0.249 950 5.07 %
Rwork0.197 --
obs0.2 18755 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2665 0 41 59 2765
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072774
X-RAY DIFFRACTIONf_angle_d1.033771
X-RAY DIFFRACTIONf_dihedral_angle_d8.0261644
X-RAY DIFFRACTIONf_chiral_restr0.058425
X-RAY DIFFRACTIONf_plane_restr0.006474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1974-2.31320.35891320.25852484X-RAY DIFFRACTION100
2.3132-2.45810.24811360.21262505X-RAY DIFFRACTION100
2.4581-2.64780.26051290.19332486X-RAY DIFFRACTION100
2.6478-2.91410.23831440.18822503X-RAY DIFFRACTION100
2.9141-3.33540.28321410.19812541X-RAY DIFFRACTION100
3.3354-4.20090.23671210.18612585X-RAY DIFFRACTION100
4.2009-33.06030.23041470.1972701X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 49.7208 Å / Origin y: 11.9347 Å / Origin z: 79.7936 Å
111213212223313233
T0.286 Å20.0661 Å2-0.0621 Å2-0.3563 Å20.0278 Å2--0.3561 Å2
L0.7391 °20.291 °20.3572 °2-0.6118 °20.0162 °2--0.9965 °2
S-0.1758 Å °0.0913 Å °0.2388 Å °0.0458 Å °-0.0017 Å °0.0874 Å °-0.2367 Å °-0.0961 Å °-0.0012 Å °
Refinement TLS groupSelection details: ALL

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