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- PDB-7was: SbSOMT in complex with pterostilbene and nicotinamide adenine din... -

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Basic information

Entry
Database: PDB / ID: 7was
TitleSbSOMT in complex with pterostilbene and nicotinamide adenine dinucleotide(NAD+)
Componentsstilbene O-methyltransferase
KeywordsTRANSFERASE / pterostilbene / 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
Pterostilbene / 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: 2.401 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 / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 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
A: stilbene O-methyltransferase
B: stilbene O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,99221
Polymers82,8052
Non-polymers3,18719
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-68 kcal/mol
Surface area30190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.469, 96.469, 169.430
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LYS / End label comp-ID: LYS / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 15 - 377 / Label seq-ID: 14 - 376

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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Protein , 1 types, 2 molecules AB

#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 , 7 types, 188 molecules

#2: Chemical ChemComp-3RL / Pterostilbene


Mass: 256.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H16O3 / 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.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 55.18 %
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: 2.401→31.421 Å / Num. obs: 36363 / % possible obs: 99.8 % / Redundancy: 19.5 % / Biso Wilson estimate: 36.78 Å2 / CC1/2: 0.915 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.046 / Rrim(I) all: 0.204 / Net I/σ(I): 7.5
Reflection shellResolution: 2.401→2.44 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.955 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1774 / CC1/2: 0.871 / Rpim(I) all: 0.228 / Rrim(I) all: 0.982 / % possible all: 99.9

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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: 2.401→31.421 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.24 / WRfactor Rwork: 0.181 / SU B: 6.812 / SU ML: 0.163 / Average fsc free: 0.9597 / Average fsc work: 0.9768 / Cross valid method: FREE R-VALUE / ESU R: 0.364 / ESU R Free: 0.255
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2462 1899 5.273 %
Rwork0.1873 34113 -
all0.19 --
obs-36012 99.138 %
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: 43.738 Å2
Baniso -1Baniso -2Baniso -3
1--0.756 Å2-0.378 Å20 Å2
2---0.756 Å20 Å2
3---2.451 Å2
Refinement stepCycle: LAST / Resolution: 2.401→31.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5622 0 214 169 6005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0126058
X-RAY DIFFRACTIONr_bond_other_d0.0030.0165572
X-RAY DIFFRACTIONr_angle_refined_deg1.9931.648210
X-RAY DIFFRACTIONr_angle_other_deg0.6511.5512951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8635746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.2171034
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67410995
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.66610255
X-RAY DIFFRACTIONr_chiral_restr0.0910.2930
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.026810
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021204
X-RAY DIFFRACTIONr_nbd_refined0.2210.21230
X-RAY DIFFRACTIONr_symmetry_nbd_other0.190.25219
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22869
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23158
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2205
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2570.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2150.229
X-RAY DIFFRACTIONr_nbd_other0.250.2110
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0770.29
X-RAY DIFFRACTIONr_mcbond_it6.1484.342960
X-RAY DIFFRACTIONr_mcbond_other6.1494.3412960
X-RAY DIFFRACTIONr_mcangle_it8.4956.4953714
X-RAY DIFFRACTIONr_mcangle_other8.4946.4953715
X-RAY DIFFRACTIONr_scbond_it7.7474.8883098
X-RAY DIFFRACTIONr_scbond_other7.7454.8883099
X-RAY DIFFRACTIONr_scangle_it10.3957.1454496
X-RAY DIFFRACTIONr_scangle_other10.3937.1454497
X-RAY DIFFRACTIONr_lrange_it12.9262.2636644
X-RAY DIFFRACTIONr_lrange_other12.92162.2696639
X-RAY DIFFRACTIONr_ncsr_local_group_10.1290.0510892
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.129160.05006
12AX-RAY DIFFRACTIONLocal ncs0.129160.05006
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
2.401-2.4630.2971370.22324940.22726330.9460.96499.9240.193
2.463-2.5310.261350.19224520.19525870.9630.9751000.16
2.531-2.6030.2651520.17823140.18324660.9570.9791000.153
2.603-2.6830.2681350.17323040.17824390.9540.9791000.146
2.683-2.770.221340.16122040.16523390.9660.98299.95720.136
2.77-2.8670.2271160.15321810.15622980.9670.98599.95650.129
2.867-2.9740.2311240.15820690.16221940.9680.98499.95440.136
2.974-3.0940.2481100.16720610.17121720.9620.98199.9540.148
3.094-3.230.2141160.15618910.15920090.9730.98499.90050.142
3.23-3.3860.251130.16418280.16919440.9620.98299.84570.152
3.386-3.5670.2461150.17917730.18318950.960.9899.63060.168
3.567-3.7810.231780.17916800.18217630.9640.9899.71640.172
3.781-4.0370.188820.17415870.17516750.9780.9899.64180.166
4.037-4.3550.224690.16714760.16915550.9680.98299.35690.167
4.355-4.7610.234550.19213940.19414610.9510.97499.17860.191
4.761-5.3080.25640.18912410.19213210.960.97698.78880.19
5.308-6.10.293560.26211120.26311910.9450.95498.06880.258
6.1-7.4020.401460.2569270.26210100.8790.9596.33660.254
7.402-10.1890.257390.1927360.1958180.9550.97194.74330.201
10.189-31.4210.246230.3263890.3215320.9720.93677.44360.351

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