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- PDB-7ffh: Diarylpentanoid-producing polyketide synthase (N199L mutant) -

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Basic information

Entry
Database: PDB / ID: 7ffh
TitleDiarylpentanoid-producing polyketide synthase (N199L mutant)
ComponentsType III polyketide synthase
KeywordsTRANSFERASE / diarylpentanoid / type-III polyketide synthase
Function / homologyChalcone/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 / polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / Thiolase-like / Type III polyketide synthase
Function and homology information
Biological speciesAquilaria sinensis (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMorita, H. / Wong, C.P. / Liu, Q. / Takeshi, K. / Lee, Y. / Nakashima, Y.
CitationJournal: Nat Commun / Year: 2022
Title: Identification of a diarylpentanoid-producing polyketide synthase revealing an unusual biosynthetic pathway of 2-(2-phenylethyl)chromones in agarwood.
Authors: Wang, X.H. / Gao, B.W. / Nakashima, Y. / Mori, T. / Zhang, Z.X. / Kodama, T. / Lee, Y.E. / Zhang, Z.K. / Wong, C.P. / Liu, Q.Q. / Qi, B.W. / Wang, J. / Li, J. / Liu, X. / Abe, I. / Morita, H. ...Authors: Wang, X.H. / Gao, B.W. / Nakashima, Y. / Mori, T. / Zhang, Z.X. / Kodama, T. / Lee, Y.E. / Zhang, Z.K. / Wong, C.P. / Liu, Q.Q. / Qi, B.W. / Wang, J. / Li, J. / Liu, X. / Abe, I. / Morita, H. / Tu, P.F. / Shi, S.P.
History
DepositionJul 23, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Type III polyketide synthase
B: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,6892
Polymers93,6892
Non-polymers00
Water1,58588
1
A: Type III polyketide synthase

A: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,6892
Polymers93,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5150 Å2
ΔGint-14 kcal/mol
Surface area26190 Å2
MethodPISA
2
B: Type III polyketide synthase

B: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,6892
Polymers93,6892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5120 Å2
ΔGint-17 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.405, 65.196, 108.394
Angle α, β, γ (deg.)90.000, 128.109, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

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Components

#1: Protein Type III polyketide synthase


Mass: 46844.656 Da / Num. of mol.: 2 / Mutation: N199L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquilaria sinensis (plant) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A385MEG6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.17 Å3/Da / Density % sol: 43.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl, pH 8.5, 25% PEG 8000, 0.3M KF, 4% butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.64 Å / Num. obs: 40917 / % possible obs: 99.7 % / Redundancy: 4.4 % / Biso Wilson estimate: 42.58 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 15.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 3522 / CC1/2: 0.954 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJY

4yjy


Resolution: 2.2→40.51 Å / SU ML: 0.2724 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.5323
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.258 2126 5.21 %
Rwork0.2132 38707 -
obs0.2155 40833 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.81 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5867 0 0 88 5955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085998
X-RAY DIFFRACTIONf_angle_d0.9168153
X-RAY DIFFRACTIONf_chiral_restr0.0538953
X-RAY DIFFRACTIONf_plane_restr0.00571048
X-RAY DIFFRACTIONf_dihedral_angle_d18.31632184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.34831350.30892579X-RAY DIFFRACTION99.41
2.25-2.310.33971580.28232539X-RAY DIFFRACTION99.23
2.31-2.370.32591260.27952543X-RAY DIFFRACTION99.52
2.37-2.440.29241300.25592597X-RAY DIFFRACTION99.71
2.44-2.520.31911300.25332606X-RAY DIFFRACTION99.89
2.52-2.610.31151460.25692563X-RAY DIFFRACTION99.71
2.61-2.710.36451320.27212563X-RAY DIFFRACTION98.94
2.71-2.840.3461520.27922574X-RAY DIFFRACTION99.56
2.84-2.990.28791490.26312567X-RAY DIFFRACTION99.74
2.99-3.170.29981390.24832575X-RAY DIFFRACTION99.71
3.17-3.420.24581470.24082589X-RAY DIFFRACTION99.78
3.42-3.760.26021490.22222543X-RAY DIFFRACTION99.01
3.76-4.30.25161590.18982556X-RAY DIFFRACTION98.55
4.31-5.420.21111250.16312650X-RAY DIFFRACTION99.75
5.42-40.510.18941490.1572663X-RAY DIFFRACTION99.47

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