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- PDB-7vb8: SbSOMT in complex with resveratrol and nicotinamide adenine dinuc... -

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Basic information

Entry
Database: PDB / ID: 7vb8
TitleSbSOMT in complex with resveratrol and nicotinamide adenine dinucleotide(NAD+)
Componentsstilbene O-methyltransferase
KeywordsTRANSFERASE / resveratrol / 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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / RESVERATROL / O-methyltransferase domain-containing protein
Similarity search - Component
Biological speciesSorghum bicolor (sorghum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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
DepositionAug 30, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 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 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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)86,55331
Polymers83,0672
Non-polymers3,48629
Water10,233568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17300 Å2
ΔGint-96 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.831, 96.831, 168.038
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: 41533.543 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 , 7 types, 597 molecules

#2: Chemical ChemComp-STL / RESVERATROL


Mass: 228.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H12O3 / 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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.74 Å3/Da / Density % sol: 55.13 %
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: 0.97853 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.72→48.462 Å / Num. obs: 97225 / % possible obs: 99.8 % / Redundancy: 19.4 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.02 / Rrim(I) all: 0.063 / Net I/σ(I): 30.2
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.941 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 4621 / CC1/2: 0.849 / Rpim(I) all: 0.357 / Rrim(I) all: 1.01 / % possible all: 97.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MrBUMP generated chimeric model

Resolution: 1.72→48.462 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.181 / WRfactor Rwork: 0.156 / SU B: 1.993 / SU ML: 0.063 / Average fsc free: 0.9712 / Average fsc work: 0.979 / Cross valid method: FREE R-VALUE / ESU R: 0.091 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1893 4899 5.042 %
Rwork0.1633 92260 -
all0.165 --
obs-97159 99.826 %
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: 26.372 Å2
Baniso -1Baniso -2Baniso -3
1--0.735 Å2-0.367 Å2-0 Å2
2---0.735 Å20 Å2
3---2.383 Å2
Refinement stepCycle: LAST / Resolution: 1.72→48.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 229 568 6419
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126196
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165693
X-RAY DIFFRACTIONr_angle_refined_deg1.6391.6428405
X-RAY DIFFRACTIONr_angle_other_deg0.5581.5513241
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3625772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.8171036
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.638101026
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.6710262
X-RAY DIFFRACTIONr_chiral_restr0.0830.2945
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027048
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021246
X-RAY DIFFRACTIONr_nbd_refined0.2250.21232
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.25116
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22965
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.23151
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2423
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1670.230
X-RAY DIFFRACTIONr_nbd_other0.2170.2102
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.224
X-RAY DIFFRACTIONr_mcbond_it2.8162.6043028
X-RAY DIFFRACTIONr_mcbond_other2.8162.6033027
X-RAY DIFFRACTIONr_mcangle_it3.933.8843818
X-RAY DIFFRACTIONr_mcangle_other3.9293.8843819
X-RAY DIFFRACTIONr_scbond_it4.1253.1293168
X-RAY DIFFRACTIONr_scbond_other4.1253.133169
X-RAY DIFFRACTIONr_scangle_it6.0574.5074587
X-RAY DIFFRACTIONr_scangle_other6.0574.5084588
X-RAY DIFFRACTIONr_lrange_it8.1541.8697052
X-RAY DIFFRACTIONr_lrange_other8.10740.7536929
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
1.72-1.7650.3033390.27166160.27371170.9460.95497.72380.245
1.765-1.8130.2583450.23365850.23569300.9580.9681000.204
1.813-1.8650.2333980.2163500.21167480.9640.9731000.178
1.865-1.9230.2163490.19961740.265230.970.9731000.169
1.923-1.9860.253150.19260620.19463770.9590.9761000.164
1.986-2.0550.1922900.17458690.17561590.9750.9811000.152
2.055-2.1330.2182900.17756700.17959610.9710.9899.98320.156
2.133-2.220.22900.16854270.16957170.9740.9831000.151
2.22-2.3180.1842840.15652140.15754980.980.9861000.14
2.318-2.4310.1822540.14650240.14852780.9790.9871000.133
2.431-2.5620.1882410.1547800.15250210.9770.9861000.138
2.562-2.7170.212350.15145050.15447400.9720.9861000.141
2.717-2.9040.1982090.15642850.15844940.9750.9851000.147
2.904-3.1360.1892450.16339520.16441970.9770.9841000.157
3.136-3.4340.1521710.16236990.16238700.9860.9851000.162
3.434-3.8360.1661730.15733500.15735230.9840.9861000.161
3.836-4.4250.1531900.13429390.13531290.9850.9891000.143
4.425-5.4090.1571220.13925530.1426750.9880.991000.153
5.409-7.6020.2151120.18519840.18720960.980.9821000.195
7.602-48.4620.209470.1712220.17112690.9670.9831000.191

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