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- PDB-3tsy: 4-Coumaroyl-CoA Ligase::Stilbene Synthase fusion protein -

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Basic information

Entry
Database: PDB / ID: 3tsy
Title4-Coumaroyl-CoA Ligase::Stilbene Synthase fusion protein
ComponentsFusion Protein 4-coumarate--CoA ligase 1, Resveratrol synthase
KeywordsLigase / Transferase / Fusion protein
Function / homology
Function and homology information


trihydroxystilbene synthase / trihydroxystilbene synthase activity / trans-feruloyl-CoA synthase / 4-coumarate-CoA ligase activity / (E)-caffeate-CoA ligase activity / 4-coumarate-CoA ligase / phenylpropanoid metabolic process / biosynthetic process / defense response / ATP binding / cytoplasm
Similarity search - Function
Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/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 / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain ...Chalcone/stilbene synthase, active site / Chalcone and stilbene synthases active site. / Chalcone/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 / ANL, N-terminal domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Thiolase/Chalcone synthase / Putative AMP-binding domain signature. / Peroxisomal Thiolase; Chain A, domain 1 / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Thiolase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
trihydroxystilbene synthase / 4-coumarate--CoA ligase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Vitis vinifera (wine grape)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsYi, H. / Jez, J.M.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural and Kinetic Analysis of the Unnatural Fusion Protein 4-Coumaroyl-CoA Ligase::Stilbene Synthase.
Authors: Wang, Y. / Yi, H. / Wang, M. / Yu, O. / Jez, J.M.
History
DepositionSep 13, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2012Group: Database references
Revision 1.2Oct 28, 2015Group: Source and taxonomy
Revision 1.3Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion Protein 4-coumarate--CoA ligase 1, Resveratrol synthase


Theoretical massNumber of molelcules
Total (without water)106,6311
Polymers106,6311
Non-polymers00
Water00
1
A: Fusion Protein 4-coumarate--CoA ligase 1, Resveratrol synthase

A: Fusion Protein 4-coumarate--CoA ligase 1, Resveratrol synthase


Theoretical massNumber of molelcules
Total (without water)213,2632
Polymers213,2632
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area5620 Å2
ΔGint-15 kcal/mol
Surface area63230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.554, 117.554, 243.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Fusion Protein 4-coumarate--CoA ligase 1, Resveratrol synthase / 4CL 1 / 4-coumarate--CoA ligase isoform 1 / At4CL1 / 4-coumaroyl-CoA synthase 1


Mass: 106631.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress), (gene. exp.) Vitis vinifera (wine grape)
Gene: 4CL1, At1g51680, At4CL1, F19C24.11, VvSTS, STS1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q42524, UniProt: Q2HY10, 4-coumarate-CoA ligase, trihydroxystilbene synthase

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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: 3.95 Å3/Da / Density % sol: 68.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18.5% PEG-3350, 0.24 M potassium citrate, 10 mM sarcosine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.1→49.1 Å / Num. all: 31924 / Num. obs: 31913 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX(phenix.refine: 1.7_650)model building
PHENIX(phenix.refine: 1.7_650)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.7_650phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→49.1 Å / SU ML: 0.35 / σ(F): 0.11 / Phase error: 19.22 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.208 1493 5 %
Rwork0.177 --
obs0.179 29888 93.8 %
all-31381 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.42 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-8.7599 Å20 Å2-0 Å2
2--8.7599 Å20 Å2
3----17.5198 Å2
Refinement stepCycle: LAST / Resolution: 3.1→49.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6323 0 0 0 6323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166655
X-RAY DIFFRACTIONf_angle_d1.3278767
X-RAY DIFFRACTIONf_dihedral_angle_d15.7282372
X-RAY DIFFRACTIONf_chiral_restr0.0921022
X-RAY DIFFRACTIONf_plane_restr0.0061131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.19910.26351180.23072233X-RAY DIFFRACTION82
3.1991-3.31340.3071200.23332286X-RAY DIFFRACTION86
3.3134-3.44610.25041270.21212420X-RAY DIFFRACTION89
3.4461-3.60280.2141310.19732498X-RAY DIFFRACTION92
3.6028-3.79270.22041360.17282573X-RAY DIFFRACTION94
3.7927-4.03030.23451380.16262606X-RAY DIFFRACTION96
4.0303-4.34130.1731390.14692659X-RAY DIFFRACTION97
4.3413-4.77780.17291420.13362694X-RAY DIFFRACTION98
4.7778-5.46840.20221430.16622706X-RAY DIFFRACTION98
5.4684-6.88660.22771460.19262787X-RAY DIFFRACTION99
6.8866-49.10.18471530.18762933X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.13280.2743-0.51551.3710.28451.1441-0.2288-0.22930.16870.58340.1125-0.42620.04790.12070.00080.8633-0.0163-0.24120.3491-0.02380.690990.9795-97.2048-51.6786
21.00230.3740.27250.9380.38411.2814-0.0463-0.03520.09630.36380.0856-0.1974-0.0230.10310.00010.763-0.0247-0.19220.3963-0.00790.64191.8446-96.0527-50.3838
31.2157-0.3085-0.87830.788-0.17920.779-0.1161-0.12940.04290.9370.04950.2139-0.15810.0499-0.00431.03850.0688-0.03480.39860.01670.487976.8027-107.7928-40.3574
41.2992-0.2376-0.24160.1201-0.27422.8318-0.0504-0.4010.17740.66480.402-0.1397-0.1736-0.13880.01970.2530.0610.08810.35650.01320.351753.0377-44.531615.8104
51.041-0.51050.1190.98510.17392.7184-0.0015-0.02970.07450.2770.13720.00870.4526-0.4257-00.4302-0.0496-0.01750.46290.07260.451648.6246-57.608311.0273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resseq 45:174)
2X-RAY DIFFRACTION2chain A and (resseq 175:281)
3X-RAY DIFFRACTION3chain A and (resseq 282:482)
4X-RAY DIFFRACTION4chain A and (resseq 589:704)
5X-RAY DIFFRACTION5chain A and (resseq 705:978)

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