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- PDB-7ffi: Diarylpentanoid-producing polyketide synthase (F340W mutant) -

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Basic information

Entry
Database: PDB / ID: 7ffi
TitleDiarylpentanoid-producing polyketide synthase (F340W mutant)
ComponentsType III polyketide synthase
KeywordsTRANSFERASE / diarylpentanoid / type-III polyketide synthase
Function / homologyChalcone/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 / 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: 2.4 Å
AuthorsMorita, H. / Wong, C.P. / Liu, Q. / Kodama, T. / 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)93,7692
Polymers93,7692
Non-polymers00
Water2,180121
1
A: Type III polyketide synthase

A: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,7692
Polymers93,7692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5080 Å2
ΔGint-18 kcal/mol
Surface area26260 Å2
MethodPISA
2
B: Type III polyketide synthase

B: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,7692
Polymers93,7692
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5170 Å2
ΔGint-15 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.245, 65.137, 108.628
Angle α, β, γ (deg.)90.000, 128.234, 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

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Components

#1: Protein Type III polyketide synthase


Mass: 46884.637 Da / Num. of mol.: 2 / Mutation: F340W
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.: 121 / 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: 2.18 Å3/Da / Density % sol: 43.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-HCl, pH 8.5, 24% PEG 8000, 0.24M 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-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.4→42.66 Å / Num. obs: 31732 / % possible obs: 99.7 % / Redundancy: 3.6 % / Biso Wilson estimate: 39.72 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3324 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7FFA

7ffa


Resolution: 2.4→42.66 Å / SU ML: 0.3522 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.5001
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2584 1589 5.02 %
Rwork0.2065 30045 -
obs0.209 31634 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.19 Å2
Refinement stepCycle: LAST / Resolution: 2.4→42.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5908 0 0 121 6029
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00276032
X-RAY DIFFRACTIONf_angle_d0.5388195
X-RAY DIFFRACTIONf_chiral_restr0.0409948
X-RAY DIFFRACTIONf_plane_restr0.00331049
X-RAY DIFFRACTIONf_dihedral_angle_d22.07272205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.480.3391320.27442706X-RAY DIFFRACTION99.4
2.48-2.570.34391390.27322684X-RAY DIFFRACTION99.47
2.57-2.670.39211350.27592729X-RAY DIFFRACTION98.9
2.67-2.790.31281490.25752738X-RAY DIFFRACTION99.14
2.79-2.940.31891500.25652696X-RAY DIFFRACTION99.44
2.94-3.120.34121330.25582713X-RAY DIFFRACTION98.99
3.12-3.360.26511520.23652719X-RAY DIFFRACTION99.17
3.36-3.70.25891520.20882701X-RAY DIFFRACTION99.13
3.7-4.240.23521600.1812743X-RAY DIFFRACTION99.79
4.24-5.330.18481250.1582799X-RAY DIFFRACTION99.83
5.33-42.660.21271620.16412817X-RAY DIFFRACTION99.67

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