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- PDB-7ffa: Diarylpentanoid-producing polyketide synthase from Aquilaria sinensis -

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Basic information

Entry
Database: PDB / ID: 7ffa
TitleDiarylpentanoid-producing polyketide synthase from Aquilaria sinensis
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: 1.98 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
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)93,7552
Polymers93,7552
Non-polymers00
Water5,278293
1
A: Type III polyketide synthase

A: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,7552
Polymers93,7552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5230 Å2
ΔGint-17 kcal/mol
Surface area25760 Å2
MethodPISA
2
B: Type III polyketide synthase

B: Type III polyketide synthase


Theoretical massNumber of molelcules
Total (without water)93,7552
Polymers93,7552
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5310 Å2
ΔGint-16 kcal/mol
Surface area25950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.996, 65.279, 107.906
Angle α, β, γ (deg.)90.000, 127.774, 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-502-

HOH

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Components

#1: Protein Type III polyketide synthase


Mass: 46877.598 Da / Num. of mol.: 2
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.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris, pH8.5, 0.12M KF, 4% butanediol, 24% PEG 8000

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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 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.98→42.65 Å / Num. obs: 56395 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 29.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.048 / Net I/σ(I): 21.9
Reflection shellResolution: 1.98→2.03 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3896 / CC1/2: 0.869 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJY

4yjy


Resolution: 1.98→42.65 Å / SU ML: 0.2385 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.4664
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 1911 3.53 %
Rwork0.1915 52160 -
obs0.1931 54071 95.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.96 Å2
Refinement stepCycle: LAST / Resolution: 1.98→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 0 293 6197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076026
X-RAY DIFFRACTIONf_angle_d0.8558186
X-RAY DIFFRACTIONf_chiral_restr0.0515948
X-RAY DIFFRACTIONf_plane_restr0.00551050
X-RAY DIFFRACTIONf_dihedral_angle_d21.17282202
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.33071140.27843201X-RAY DIFFRACTION83.08
2.03-2.080.30141430.25473328X-RAY DIFFRACTION86.62
2.08-2.140.31220.23663531X-RAY DIFFRACTION90.67
2.14-2.210.2611280.22753636X-RAY DIFFRACTION93.8
2.21-2.290.27041250.20783733X-RAY DIFFRACTION95.09
2.29-2.380.27371530.21713681X-RAY DIFFRACTION96.23
2.38-2.490.23651320.21233803X-RAY DIFFRACTION97.45
2.49-2.620.30511370.21943811X-RAY DIFFRACTION97.63
2.62-2.790.25991410.22553823X-RAY DIFFRACTION98.68
2.79-30.30391420.22113882X-RAY DIFFRACTION99.33
3-3.310.24591400.20463882X-RAY DIFFRACTION99.78
3.31-3.780.22431400.18423902X-RAY DIFFRACTION99.7
3.78-4.770.18981440.15013944X-RAY DIFFRACTION99.93
4.77-42.650.18951500.15384003X-RAY DIFFRACTION99.57

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