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- PDB-9lym: Functional characterization of type III polyketide synthases invo... -

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Basic information

Entry
Database: PDB / ID: 9lym
TitleFunctional characterization of type III polyketide synthases involved in tropane alkaloid biosynthesis in Brassicaceae
ComponentsChalcone synthase
KeywordsBIOSYNTHETIC PROTEIN / type III polyketide synthases / tropane alkaloid / biosynthesis / Brassicaceae
Function / homology
Function and homology information


polyketide biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / endoplasmic reticulum
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/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 / Thiolase-like
Similarity search - Domain/homology
COENZYME A / Chalcone synthase
Similarity search - Component
Biological speciesCochlearia officinalis (scurvy-grass)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsYan, Y.J. / Huang, S.X.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB27020205 China
CitationJournal: To Be Published
Title: Biosynthesis of Panaradisoquinolines reveals an Enoyl Coenzyme A Hydratase-mediated cascade reactions for the formation of isoquinoline scaffold
Authors: Yan, Y.J. / Huang, S.X.
History
DepositionFeb 20, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Chalcone synthase
BA: Chalcone synthase
CA: Chalcone synthase
DA: Chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,6217
Polymers172,3184
Non-polymers2,3033
Water11,728651
1
AA: Chalcone synthase
CA: Chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9273
Polymers86,1592
Non-polymers7681
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-11 kcal/mol
Surface area26900 Å2
MethodPISA
2
BA: Chalcone synthase
DA: Chalcone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,6944
Polymers86,1592
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-20 kcal/mol
Surface area26520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.200, 264.660, 73.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein
Chalcone synthase


Mass: 43079.594 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cochlearia officinalis (scurvy-grass) / Gene: chs
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A173QN86
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 46.04 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.2M Sodium chloride, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.15→34.28 Å / Num. obs: 86731 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 38.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.051 / Net I/σ(I): 15
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 1.393 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8510 / CC1/2: 0.714 / Rpim(I) all: 0.57 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0023refinement
XDSBUILT=20230630data reduction
MOLREP11.0/22.07.2010/phasing
Aimless0.7.6data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→34.28 Å / SU ML: 0.2588 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2398 2000 2.31 %
Rwork0.174 84640 -
obs0.1755 86640 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.27 Å2
Refinement stepCycle: LAST / Resolution: 2.15→34.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11944 0 144 651 12739
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012412326
X-RAY DIFFRACTIONf_angle_d1.187216701
X-RAY DIFFRACTIONf_chiral_restr0.05921897
X-RAY DIFFRACTIONf_plane_restr0.01022131
X-RAY DIFFRACTIONf_dihedral_angle_d9.88981740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.20.31441400.24285956X-RAY DIFFRACTION100
2.2-2.260.30631410.22355946X-RAY DIFFRACTION100
2.26-2.330.30071410.21495976X-RAY DIFFRACTION100
2.33-2.410.29621410.20955958X-RAY DIFFRACTION100
2.41-2.490.29311420.20485990X-RAY DIFFRACTION100
2.49-2.590.30031410.19915984X-RAY DIFFRACTION100
2.59-2.710.24291430.26038X-RAY DIFFRACTION99.97
2.71-2.850.30651410.19865973X-RAY DIFFRACTION100
2.85-3.030.27931430.20756052X-RAY DIFFRACTION100
3.03-3.260.30091430.20586031X-RAY DIFFRACTION100
3.26-3.590.24721430.1786044X-RAY DIFFRACTION100
3.59-4.110.24231430.15166118X-RAY DIFFRACTION100
4.11-5.180.14961470.12456169X-RAY DIFFRACTION99.97
5.18-34.280.19341510.1556405X-RAY DIFFRACTION99.8

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