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- PDB-6gw3: Structure of TKS from Cannabis sativa in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 6gw3
TitleStructure of TKS from Cannabis sativa in complex with CoA
Components
  • 3,5,7-trioxododecanoyl-CoA synthase
  • 3,5,7-trioxododecanoyl-CoA synthase,3,5,7-trioxododecanoyl-CoA synthase
KeywordsLIGASE / 3 / 5 / 7-trioxododecanoyl-CoA synthase / polyketide synthase / PKS type III
Function / homology
Function and homology information


3,5,7-trioxododecanoyl-CoA synthase / Lyases; Carbon-sulfur lyases / cannabinoid biosynthetic process / polyketide biosynthetic process / terpenoid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups / lyase activity
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/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like ...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/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / DI(HYDROXYETHYL)ETHER / 3,5,7-trioxododecanoyl-CoA synthase
Similarity search - Component
Biological speciesCannabis sativa (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsKaruppiah, V. / Leys, D.
CitationJournal: To Be Published
Title: Structure of a PKS class III from Cannabis sativa
Authors: Kearsey, L. / Karuppiah, V. / Leys, D. / Takano, E. / Scrutton, N.S.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3,5,7-trioxododecanoyl-CoA synthase
B: 3,5,7-trioxododecanoyl-CoA synthase
C: 3,5,7-trioxododecanoyl-CoA synthase
D: 3,5,7-trioxododecanoyl-CoA synthase,3,5,7-trioxododecanoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)186,54310
Polymers183,2614
Non-polymers3,2826
Water22,6271256
1
A: 3,5,7-trioxododecanoyl-CoA synthase
B: 3,5,7-trioxododecanoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,4946
Polymers85,7472
Non-polymers1,7474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 3,5,7-trioxododecanoyl-CoA synthase
D: 3,5,7-trioxododecanoyl-CoA synthase,3,5,7-trioxododecanoyl-CoA synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0494
Polymers97,5142
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.560, 123.288, 87.939
Angle α, β, γ (deg.)90.00, 109.55, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISTYRTYRAA3 - 3856 - 388
21HISHISTYRTYRBB3 - 3856 - 388
12LEULEULYSLYSAA4 - 3847 - 387
22LEULEULYSLYSCC4 - 3847 - 387
13LEULEUPROPROAA4 - 3827 - 385
23LEULEUPROPRODD4 - 382108 - 486
14LEULEULYSLYSBB4 - 3847 - 387
24LEULEULYSLYSCC4 - 3847 - 387
15LEULEUPROPROBB4 - 3827 - 385
25LEULEUPROPRODD4 - 382108 - 486
16LEULEUPROPROCC4 - 3827 - 385
26LEULEUPROPRODD4 - 382108 - 486

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein 3,5,7-trioxododecanoyl-CoA synthase / Olivetol synthase / Polyketide synthase-1 / Tetraketide synthase


Mass: 42873.285 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Gene: OLS, CAN24, PKS-1, TKS / Production host: Escherichia coli (E. coli)
References: UniProt: B1Q2B6, 3,5,7-trioxododecanoyl-CoA synthase
#2: Protein 3,5,7-trioxododecanoyl-CoA synthase,3,5,7-trioxododecanoyl-CoA synthase / Olivetol synthase / Polyketide synthase-1 / Tetraketide synthase


Mass: 54640.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cannabis sativa (plant) / Gene: OLS, CAN24, PKS-1, TKS / Production host: Escherichia coli (E. coli)
References: UniProt: B1Q2B6, 3,5,7-trioxododecanoyl-CoA synthase
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1256 / Source method: isolated from a natural source / Formula: H2O
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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 279 K / Method: vapor diffusion, sitting drop / Details: 20 % PEG 20000, 0.1 M Hepes, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Dec 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.39→82.87 Å / Num. obs: 280655 / % possible obs: 98.4 % / Redundancy: 3.3 % / Net I/σ(I): 13.7
Reflection shellResolution: 1.39→1.42 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 13838 / CC1/2: 0.8 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0069refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YJY

4yjy


Resolution: 1.39→82.87 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.93 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.052 / ESU R Free: 0.05 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15469 13987 5 %RANDOM
Rwork0.11831 ---
obs0.12012 266625 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 21.959 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20.23 Å2
2---0.46 Å20 Å2
3---0.28 Å2
Refinement stepCycle: 1 / Resolution: 1.39→82.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11839 0 206 1256 13301
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01912554
X-RAY DIFFRACTIONr_bond_other_d0.0090.0212157
X-RAY DIFFRACTIONr_angle_refined_deg1.7911.99217019
X-RAY DIFFRACTIONr_angle_other_deg1.516328146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1210.21907
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02114021
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022699
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1621.7846246
X-RAY DIFFRACTIONr_mcbond_other2.1481.7846245
X-RAY DIFFRACTIONr_mcangle_it2.4892.6777841
X-RAY DIFFRACTIONr_mcangle_other2.4922.6787842
X-RAY DIFFRACTIONr_scbond_it4.9762.3416308
X-RAY DIFFRACTIONr_scbond_other4.9762.3416309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2953.3179164
X-RAY DIFFRACTIONr_long_range_B_refined4.75720.83410077
X-RAY DIFFRACTIONr_long_range_B_other4.75620.83410078
X-RAY DIFFRACTIONr_rigid_bond_restr6.801324707
X-RAY DIFFRACTIONr_sphericity_free34.8995360
X-RAY DIFFRACTIONr_sphericity_bonded13.154525333
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A237700.1
12B237700.1
21A238880.08
22C238880.08
31A235130.09
32D235130.09
41B238120.09
42C238120.09
51B238700.08
52D238700.08
61C232220.1
62D232220.1
LS refinement shellResolution: 1.394→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 1022 -
Rwork0.205 19514 -
obs--97.27 %

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