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- PDB-6op5: Crystal Structure of Piper methysticum Styrylpyrone Synthase 1 in... -

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Basic information

Entry
Database: PDB / ID: 6op5
TitleCrystal Structure of Piper methysticum Styrylpyrone Synthase 1 in complex with p-coumaroyl-CoA
Components(Styrylpyrone synthase 1) x 2
KeywordsTRANSFERASE / kavalactone biosynthesis / phenylpropanoid pathway
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Chalcone and stilbene synthases, N-terminal domain / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
p-coumaroyl-CoA / Styrylpyrone synthase 1
Similarity search - Component
Biological speciesPiper methysticum (kava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPluskal, T. / Weng, J.K.
CitationJournal: Nat.Plants / Year: 2019
Title: The biosynthetic origin of psychoactive kavalactones in kava.
Authors: Pluskal, T. / Torrens-Spence, M.P. / Fallon, T.R. / De Abreu, A. / Shi, C.H. / Weng, J.K.
History
DepositionApr 24, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionJun 12, 2019ID: 6CO0
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Apr 2, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Styrylpyrone synthase 1
B: Styrylpyrone synthase 1
C: Styrylpyrone synthase 1
D: Styrylpyrone synthase 1
E: Styrylpyrone synthase 1
F: Styrylpyrone synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,4428
Polymers261,6156
Non-polymers1,8272
Water3,279182
1
A: Styrylpyrone synthase 1
B: Styrylpyrone synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,9844
Polymers87,1562
Non-polymers1,8272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Styrylpyrone synthase 1
D: Styrylpyrone synthase 1


Theoretical massNumber of molelcules
Total (without water)87,3022
Polymers87,3022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Styrylpyrone synthase 1
F: Styrylpyrone synthase 1


Theoretical massNumber of molelcules
Total (without water)87,1562
Polymers87,1562
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)164.402, 164.402, 87.122
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3

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Components

#1: Protein
Styrylpyrone synthase 1


Mass: 43578.160 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piper methysticum (kava) / Plasmid: pHis8-4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A384E132
#2: Protein Styrylpyrone synthase 1


Mass: 43724.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piper methysticum (kava) / Plasmid: pHis8-4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A384E132
#3: Chemical ChemComp-WCA / p-coumaroyl-CoA


Mass: 913.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H42N7O18P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.64 % / Description: needle
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES pH 7.5, PEG 8000 10% w/v, ethylene glycol 4% v/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.7→82.201 Å / Num. obs: 142832 / % possible obs: 98.75 % / Redundancy: 6.2 % / Net I/σ(I): 7.1
Reflection shellResolution: 2.7→2.797 Å / Num. unique obs: 6973

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIX1.14_3260phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→82.201 Å / Cross valid method: FREE R-VALUE / σ(F): 2.61 / Phase error: 28.19
RfactorNum. reflection% reflection
Rfree0.2612 3972 2.78 %
Rwork0.2042 --
obs0.2114 142832 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→82.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17620 0 118 182 17920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418089
X-RAY DIFFRACTIONf_angle_d0.68124523
X-RAY DIFFRACTIONf_dihedral_angle_d5.57110891
X-RAY DIFFRACTIONf_chiral_restr0.0452812
X-RAY DIFFRACTIONf_plane_restr0.0053142
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7008-2.74730.29671960.25936973X-RAY DIFFRACTION97
2.7473-2.79730.32351990.25776849X-RAY DIFFRACTION94
2.7973-2.85110.33211980.25326860X-RAY DIFFRACTION95
2.8511-2.90930.29191990.25397019X-RAY DIFFRACTION97
2.9093-2.97260.2831980.2516965X-RAY DIFFRACTION97
2.9726-3.04170.30042160.24827064X-RAY DIFFRACTION96
3.0417-3.11780.26541950.24326955X-RAY DIFFRACTION97
3.1178-3.20210.32371830.24066964X-RAY DIFFRACTION97
3.2021-3.29630.30662000.23416965X-RAY DIFFRACTION97
3.2963-3.40270.32871960.2296949X-RAY DIFFRACTION96
3.4027-3.52430.26041820.22376784X-RAY DIFFRACTION94
3.5243-3.66530.27521910.21687033X-RAY DIFFRACTION97
3.6653-3.83210.25182020.20426944X-RAY DIFFRACTION97
3.8321-4.03410.28452000.20086983X-RAY DIFFRACTION96
4.0341-4.28680.27682080.17926986X-RAY DIFFRACTION97
4.2868-4.61770.22111880.16636754X-RAY DIFFRACTION93
4.6177-5.08220.25181960.16716996X-RAY DIFFRACTION97
5.0822-5.8170.21262080.19337061X-RAY DIFFRACTION97
5.817-7.32680.23962000.2036801X-RAY DIFFRACTION95
7.3268-59.80360.23851840.20276908X-RAY DIFFRACTION96

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