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- PDB-9grr: Crystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (... -

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Basic information

Entry
Database: PDB / ID: 9grr
TitleCrystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (At-FatA) complexed with Cinmethylin
ComponentsOleoyl-acyl carrier protein thioesterase 1, chloroplastic
KeywordsHYDROLASE / Thioesterase / Herbicide / Inhibitor / Cinmethylin
Function / homology
Function and homology information


oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / chloroplast / fatty acid biosynthetic process
Similarity search - Function
Acyl-ACP thioesterase / Acyl-[acyl-carrier-protein] hydrolase FATA/B / : / Acyl-ACP thioesterase N-terminal domain / Acyl-ACP thioesterase C-terminal domain / HotDog domain superfamily
Similarity search - Domain/homology
: / Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMontgomery, M.G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Scaffold-hopping, Bioisosterism and Structure-Based Design in the Development of Novel Acyl-ACP Thioesterase (Fat) Inhibitors as Potential Herbicides
Authors: Croft, R. / Montgomery, M.G.
History
DepositionSep 12, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AaA: Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1745
Polymers33,6161
Non-polymers5594
Water2,864159
1
AaA: Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
hetero molecules

AaA: Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,34810
Polymers67,2312
Non-polymers1,1178
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_445-y-1/2,-x-1/2,-z+1/21
Unit cell
Length a, b, c (Å)98.430, 98.430, 126.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11AaA-402-

SO4

21AaA-645-

HOH

31AaA-654-

HOH

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Components

#1: Protein Oleoyl-acyl carrier protein thioesterase 1, chloroplastic / 18:0-acyl-carrier protein thioesterase / 18:0-ACP thioesterase / Acyl-[acyl-carrier-protein] hydrolase


Mass: 33615.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FATA, FATA1, At3g25110, MJL12.5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q42561, oleoyl-[acyl-carrier-protein] hydrolase
#2: Chemical ChemComp-A1IOW / (1~{S},2~{R},4~{R})-1-methyl-2-[(2-methylphenyl)methoxy]-4-propan-2-yl-7-oxabicyclo[2.2.1]heptane


Mass: 274.398 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H26O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / 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: 2.27 Å3/Da / Density % sol: 45.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.3M ammonium sulphate, 0.1M sodium acetate pH 4.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9159 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9159 Å / Relative weight: 1
ReflectionResolution: 1.4→77.61 Å / Num. obs: 59353 / % possible obs: 97.4 % / Redundancy: 8.8 % / CC1/2: 1 / Rrim(I) all: 0.056 / Net I/σ(I): 16.6
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2943 / CC1/2: 0.5 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→77.607 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.322 / SU ML: 0.052 / Cross valid method: FREE R-VALUE / ESU R: 0.069 / ESU R Free: 0.068
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2329 3014 5.079 %
Rwork0.2161 56334 -
all0.217 --
obs-59348 97.367 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 24.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.015 Å2-0 Å20 Å2
2--0.015 Å2-0 Å2
3----0.029 Å2
Refinement stepCycle: LAST / Resolution: 1.4→77.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2080 0 36 159 2275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132217
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172042
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.6423016
X-RAY DIFFRACTIONr_angle_other_deg1.4911.584734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0815270
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23821.732127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82615391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1211519
X-RAY DIFFRACTIONr_chiral_restr0.0820.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022445
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02480
X-RAY DIFFRACTIONr_nbd_refined0.20.2361
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21839
X-RAY DIFFRACTIONr_nbtor_refined0.1660.21024
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21021
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2108
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2430.215
X-RAY DIFFRACTIONr_nbd_other0.1850.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.220
X-RAY DIFFRACTIONr_mcbond_it2.032.3551053
X-RAY DIFFRACTIONr_mcbond_other2.0222.3521052
X-RAY DIFFRACTIONr_mcangle_it2.9793.5261314
X-RAY DIFFRACTIONr_mcangle_other2.983.5291315
X-RAY DIFFRACTIONr_scbond_it2.732.6881164
X-RAY DIFFRACTIONr_scbond_other2.7292.6891165
X-RAY DIFFRACTIONr_scangle_it4.173.8981696
X-RAY DIFFRACTIONr_scangle_other4.1693.8991697
X-RAY DIFFRACTIONr_lrange_it5.4227.1662410
X-RAY DIFFRACTIONr_lrange_other5.3927.0182394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.3312240.3341150.33144400.7570.73897.72520.326
1.436-1.4760.3232150.30940310.30943440.8130.81497.7440.298
1.476-1.5190.2791820.28439310.28442180.8490.84797.51070.266
1.519-1.5650.2962020.26338100.26441100.8440.85497.61560.241
1.565-1.6170.2922020.23837080.24139980.8760.90297.79890.215
1.617-1.6730.2721890.23635600.23838270.90.91497.96180.213
1.673-1.7360.2831870.23434730.23737340.8990.92298.01820.209
1.736-1.8070.2211790.22333480.22335890.9370.92898.27250.202
1.807-1.8880.2341730.21931960.21934410.9260.93297.90760.198
1.888-1.980.2281800.2230420.2232850.9340.93498.08220.202
1.98-2.0870.2251600.22329420.22331570.9370.93998.25780.208
2.087-2.2130.2151490.20527680.20629760.9510.94598.01750.195
2.213-2.3660.221490.21226020.21228080.9370.93897.97010.2
2.366-2.5550.2381380.21424280.21526250.9270.93897.75240.204
2.555-2.7990.2321300.21122250.21324300.9370.94396.91360.208
2.799-3.1290.224890.21620440.21722070.9410.93996.6470.214
3.129-3.6120.242930.20617770.20819620.9410.94595.31090.213
3.612-4.4210.19780.17914950.1816750.9550.96293.91040.197
4.421-6.2420.224580.19311760.19513320.9690.96892.64260.221
6.242-77.6070.224370.2436630.2427950.930.94188.05030.272

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