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- PDB-6nbr: Crystal Structure of Piper methysticum Kavalactone Reductase 1 in... -

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Basic information

Entry
Database: PDB / ID: 6nbr
TitleCrystal Structure of Piper methysticum Kavalactone Reductase 1 in complex with NADP
ComponentsKavalactone reductase 1
KeywordsTRANSFERASE / phenylpropanoid pathway / kavalactone biosynthesis
Function / homology
Function and homology information


NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Kavalactone reductase 1
Similarity search - Component
Biological speciesPiper methysticum (kava)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionDec 9, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 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
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kavalactone reductase 1
B: Kavalactone reductase 1
C: Kavalactone reductase 1
D: Kavalactone reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,0618
Polymers146,0874
Non-polymers2,9744
Water88349
1
A: Kavalactone reductase 1
C: Kavalactone reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5304
Polymers73,0442
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: Kavalactone reductase 1
C: Kavalactone reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5304
Polymers73,0442
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Kavalactone reductase 1
D: Kavalactone reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5304
Polymers73,0442
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Kavalactone reductase 1
D: Kavalactone reductase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5304
Polymers73,0442
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.220, 63.239, 333.746
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein
Kavalactone reductase 1


Mass: 36521.809 Da / Num. of mol.: 4
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: A0A4Y5QR90*PLUS
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.28 Å3/Da / Density % sol: 46.13 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: NH4Ac 0.35 M, HEPES 0.1M, PEG 3350 25% w/v

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→83.44 Å / Num. obs: 33052 / % possible obs: 96.9 % / Redundancy: 10.8 % / Net I/σ(I): 8.2
Reflection shellResolution: 2.8→2.94 Å / Num. unique obs: 3212

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Phyre2 model

Resolution: 2.8→62.13 Å / Cross valid method: FREE R-VALUE / σ(F): 101 / Phase error: 26.3238
RfactorNum. reflection% reflection
Rfree0.2608 3444 10.47 %
Rwork0.2179 --
obs0.2375 32903 96.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 67.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→62.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9874 0 192 49 10115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005610285
X-RAY DIFFRACTIONf_angle_d0.790113976
X-RAY DIFFRACTIONf_chiral_restr0.04811602
X-RAY DIFFRACTIONf_plane_restr0.00441728
X-RAY DIFFRACTIONf_dihedral_angle_d22.79523740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.850.32861740.32181415X-RAY DIFFRACTION84.13
2.85-2.90.37381570.31981446X-RAY DIFFRACTION85.77
2.9-2.960.36891640.32741407X-RAY DIFFRACTION85.43
2.96-3.020.35191430.30451453X-RAY DIFFRACTION85.37
3.02-3.080.28571700.30211428X-RAY DIFFRACTION86.13
3.08-3.150.34171720.30421411X-RAY DIFFRACTION83.99
3.15-3.230.30171700.30781390X-RAY DIFFRACTION85.02
3.23-3.320.34031540.29131456X-RAY DIFFRACTION84.55
3.32-3.420.28791500.27171419X-RAY DIFFRACTION86.63
3.42-3.530.32081980.26611406X-RAY DIFFRACTION81.65
3.53-3.650.28521510.25081413X-RAY DIFFRACTION85.84
3.65-3.80.28451450.25031472X-RAY DIFFRACTION85.98
3.8-3.970.26781600.22941474X-RAY DIFFRACTION85.9
3.97-4.180.25441870.21741492X-RAY DIFFRACTION87.71
4.18-4.440.23541600.20821520X-RAY DIFFRACTION90.1
4.44-4.780.25911570.1971539X-RAY DIFFRACTION90.11
4.78-5.260.25441830.19651584X-RAY DIFFRACTION89.64
5.26-6.020.2341780.21361520X-RAY DIFFRACTION89.52
6.02-7.560.26861700.19661606X-RAY DIFFRACTION90.38
7.56-30.420.2341800.19751693X-RAY DIFFRACTION89.86

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