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- PDB-6cqb: Crystal Structure of Piper methysticum Chalcone Synthase -

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Basic information

Entry
Database: PDB / ID: 6cqb
TitleCrystal Structure of Piper methysticum Chalcone Synthase
ComponentsChalcone synthase
KeywordsTRANSFERASE / phenylpropanoid pathway / flavokavain biosynthesis
Function / homology
Function and homology information


biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups
Similarity search - Function
Chalcone/stilbene synthase, N-terminal / Polyketide synthase, type III / Chalcone/stilbene synthase, C-terminal / Chalcone and stilbene synthases, C-terminal domain / Chalcone and stilbene synthases, N-terminal domain / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPiper methysticum (kava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.91 Å
AuthorsPluskal, T. / Weng, J.K.
Funding support United States, 7items
OrganizationGrant numberCountry
Edward N. and Della L. Thome Memorial Foundation United States
Family Larsson-Rosenquist Foundation United States
Arnold and Mabel Beckman Foundation United States
National Science Foundation (NSF, United States)1709616 United States
Pew Charitable Trusts27345 United States
Chicago Community Trust15-SSP-162 United States
Helen Hay Whitney FoundationF-1055 United States
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
DepositionMar 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: 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
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chalcone synthase
B: Chalcone synthase


Theoretical massNumber of molelcules
Total (without water)86,0852
Polymers86,0852
Non-polymers00
Water61334
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-2 kcal/mol
Surface area26870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.910, 120.570, 125.408
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Chalcone synthase


Mass: 43042.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piper methysticum (kava) / Gene: CHS / Organ: Root / Plasmid: pHIS8-4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A384E133*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 44.98 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES 100 mM pH 7.0, PEG 6000 10% w/v

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.91→62.704 Å / Num. obs: 17602 / % possible obs: 99.95 % / Redundancy: 61.6 % / Net I/σ(I): 12.54
Reflection shellResolution: 2.91→3.014 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phyre2 model

Resolution: 2.91→62.704 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.64
RfactorNum. reflection% reflection
Rfree0.3162 1771 10.06 %
Rwork0.2626 --
obs0.2679 17602 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.91→62.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5824 0 0 34 5858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025965
X-RAY DIFFRACTIONf_angle_d0.5288086
X-RAY DIFFRACTIONf_dihedral_angle_d16.1513615
X-RAY DIFFRACTIONf_chiral_restr0.041930
X-RAY DIFFRACTIONf_plane_restr0.0031042
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.91-2.98870.36611440.33851195X-RAY DIFFRACTION100
2.9887-3.07660.37141230.33011181X-RAY DIFFRACTION100
3.0766-3.17590.3461410.31111194X-RAY DIFFRACTION100
3.1759-3.28940.35751290.2951191X-RAY DIFFRACTION100
3.2894-3.42110.32181340.28461212X-RAY DIFFRACTION100
3.4211-3.57680.35661310.27051202X-RAY DIFFRACTION100
3.5768-3.76540.30521380.27441198X-RAY DIFFRACTION100
3.7654-4.00120.31711400.25661199X-RAY DIFFRACTION100
4.0012-4.31010.29711310.22921221X-RAY DIFFRACTION100
4.3101-4.74370.26861330.21651221X-RAY DIFFRACTION100
4.7437-5.42980.26271430.21771233X-RAY DIFFRACTION100
5.4298-6.83970.31141420.2671242X-RAY DIFFRACTION100
6.8397-62.71850.32841420.25491342X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3556-0.2576-0.05310.19250.00881.20930.2073-0.02390.1077-0.18830.03440.0646-0.3537-0.01240.49610.4718-0.0498-0.24550.51420.60980.632997.0896154.0484142.748
20.1915-0.2259-0.11420.30940.17491.27140.13540.00520.1369-0.24380.083-0.0615-0.49260.22410.5240.4423-0.01190.02090.60890.51390.6728105.8549149.7977144.8711
30.0860.03890.01490.11890.11190.12060.04340.0332-0.0112-0.22720.0135-0.01760.18210.03450.08050.59490.0067-0.03790.42640.63880.3971110.1483139.1613135.3794
40.6830.1029-0.2520.09610.28821.55860.02550.03360.1862-0.2077-0.09440.12-0.4738-0.12060.03110.1918-0.0297-0.10420.260.23040.52599.6662155.3419176.197
51.8587-0.2354-0.51610.16080.49921.58840.0230.32970.6502-0.04460.12840.0271-0.4993-0.41510.00750.26790.069-0.03930.58720.26620.925100.8043162.1536174.7117
60.34850.05710.40010.0838-0.13921.0446-0.11110.0860.24980.00190.05420.0968-0.2514-0.2161-0.06530.10140.1037-0.10930.30410.58780.3101102.9673148.1947165.2752
71.16520.10780.67130.3427-0.1690.83440.02650.34240.287-0.02470.00470.0218-0.15870.03820.00040.24470.1149-0.14470.52630.25530.732490.5452146.1155167.154
80.30460.1191-0.04420.80030.55360.76010.1339-0.0725-0.15420.21360.0720.17910.2314-0.29340.02590.1661-0.00460.09370.46740.4030.632589.3188139.1476178.2423
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 181 )
2X-RAY DIFFRACTION2chain 'A' and (resid 182 through 279 )
3X-RAY DIFFRACTION3chain 'A' and (resid 280 through 390 )
4X-RAY DIFFRACTION4chain 'B' and (resid 10 through 50 )
5X-RAY DIFFRACTION5chain 'B' and (resid 51 through 118 )
6X-RAY DIFFRACTION6chain 'B' and (resid 119 through 226 )
7X-RAY DIFFRACTION7chain 'B' and (resid 227 through 279 )
8X-RAY DIFFRACTION8chain 'B' and (resid 280 through 390 )

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