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- PDB-7war: SbSOMT in complex with pinostilbene and nicotinamide adenine dinu... -

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Basic information

Entry
Database: PDB / ID: 7war
TitleSbSOMT in complex with pinostilbene and nicotinamide adenine dinucleotide(NAD+)
Componentsstilbene O-methyltransferase
KeywordsTRANSFERASE / pinostilbene / complex / o-methyltransferase / substrate
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / O-methyltransferase activity / biosynthetic process / methylation / protein dimerization activity / nucleotide binding
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
Chem-8KZ / ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.101 Å
AuthorsPow, K.C. / Hao, Q.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Nat Commun / Year: 2023
Title: Regioselective stilbene O-methylations in Saccharinae grasses.
Authors: Lui, A.C.W. / Pow, K.C. / Lin, N. / Lam, L.P.Y. / Liu, G. / Godwin, I.D. / Fan, Z. / Khoo, C.J. / Tobimatsu, Y. / Wang, L. / Hao, Q. / Lo, C.
History
DepositionDec 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Structure summary / Category: citation / struct / Item: _citation.title / _struct.title
Revision 1.2Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: stilbene O-methyltransferase
A: stilbene O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,90832
Polymers82,8052
Non-polymers4,10430
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18540 Å2
ΔGint-64 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.700, 96.700, 166.900
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein stilbene O-methyltransferase


Mass: 41402.348 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorghum bicolor (sorghum) / Gene: SORBI_3007G059100 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3) RIL / References: UniProt: A0A1B6PFV1

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Non-polymers , 8 types, 298 molecules

#2: Chemical ChemComp-8KZ / 3-[(E)-2-(4-hydroxyphenyl)ethenyl]-5-methoxy-phenol / Pinostilbene


Mass: 242.270 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H14O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.2 M sodium acetate , 0.2 M ammonium chloride, 2.5% (w/v) polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9784 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 2.101→19.712 Å / Num. obs: 53180 / % possible obs: 99.8 % / Redundancy: 6.4 % / Biso Wilson estimate: 31.43 Å2 / CC1/2: 0.891 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.094 / Rrim(I) all: 0.238 / Net I/σ(I): 9.2
Reflection shellResolution: 2.101→2.14 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 2 / Num. unique obs: 5048 / CC1/2: 0.79 / Rpim(I) all: 0.31 / Rrim(I) all: 0.788 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VB8

7vb8


Resolution: 2.101→19.712 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.201 / WRfactor Rwork: 0.169 / SU B: 4.016 / SU ML: 0.105 / Average fsc free: 0.971 / Average fsc work: 0.9763 / Cross valid method: FREE R-VALUE / ESU R: 0.18 / ESU R Free: 0.152
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2025 2652 4.991 %
Rwork0.1708 50481 -
all0.172 --
obs-53133 99.67 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.983 Å2
Baniso -1Baniso -2Baniso -3
1--0.495 Å2-0.248 Å2-0 Å2
2---0.495 Å20 Å2
3---1.606 Å2
Refinement stepCycle: LAST / Resolution: 2.101→19.712 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5616 0 274 268 6158
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0126057
X-RAY DIFFRACTIONr_bond_other_d0.0030.0165603
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.648183
X-RAY DIFFRACTIONr_angle_other_deg0.6771.5513016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.285737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.2561034
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.12110985
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.33510251
X-RAY DIFFRACTIONr_chiral_restr0.1010.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.026737
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021197
X-RAY DIFFRACTIONr_nbd_refined0.2230.21246
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.25374
X-RAY DIFFRACTIONr_nbtor_refined0.1840.22888
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.23204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1730.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1880.229
X-RAY DIFFRACTIONr_nbd_other0.2350.294
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.217
X-RAY DIFFRACTIONr_mcbond_it4.4983.4442935
X-RAY DIFFRACTIONr_mcbond_other4.4953.4442934
X-RAY DIFFRACTIONr_mcangle_it5.9955.1473675
X-RAY DIFFRACTIONr_mcangle_other5.9955.1473676
X-RAY DIFFRACTIONr_scbond_it6.2983.9913122
X-RAY DIFFRACTIONr_scbond_other6.2973.9913123
X-RAY DIFFRACTIONr_scangle_it8.8565.794508
X-RAY DIFFRACTIONr_scangle_other8.8555.7914509
X-RAY DIFFRACTIONr_lrange_it10.50151.166700
X-RAY DIFFRACTIONr_lrange_other10.50550.5466676
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.101-2.1550.2171760.20836040.20938240.9680.97198.84940.194
2.155-2.2140.21800.19736020.19737820.9690.9741000.179
2.214-2.2770.3711640.34434830.34636470.8890.8971000.326
2.277-2.3460.2021610.16333730.16535340.9770.9821000.145
2.346-2.4220.1812050.15332570.15534620.980.9851000.134
2.422-2.5060.1831650.14531760.14733410.9790.9871000.127
2.506-2.5990.1881750.15730370.15932120.9770.9851000.138
2.599-2.7030.2011260.15529950.15731210.9750.9851000.135
2.703-2.820.1831650.13828140.1429790.9790.9881000.124
2.82-2.9550.1781050.13327600.13528650.980.9891000.121
2.955-3.1110.2051220.13926460.14227680.9750.9881000.13
3.111-3.2950.1831610.14223990.14525600.9790.9871000.137
3.295-3.5150.181420.15523340.15624760.980.9851000.152
3.515-3.7870.1811260.16121640.16222900.980.9841000.16
3.787-4.1330.196850.16420410.16521270.9740.98399.9530.169
4.133-4.5960.185940.16518570.16619520.980.98199.94880.178
4.596-5.2590.2181080.17116220.17417330.9740.98399.82690.188
5.259-6.3290.2381080.2113920.21215040.980.97599.7340.227
6.329-8.5220.196470.18911680.1912250.980.97599.18370.212
8.522-19.7120.262370.2327570.2338220.9550.95296.59370.292

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