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

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Basic information

Entry
Database: PDB / ID: 9hmt
TitleCrystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (At-FatA) complexed with methiozolin-fluorine
ComponentsOleoyl-acyl carrier protein thioesterase 1, chloroplastic
KeywordsHYDROLASE / Arabidopsis / Thioesterase / Inhibitor / Herbicide / Methiozolin
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: 1.38 Å
AuthorsMontgomery, M.G.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Crystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (At-FatA) complexed with methiozolin-fluorine
Authors: Montgomery, M.G.
History
DepositionDec 9, 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)34,1394
Polymers33,6161
Non-polymers5233
Water3,045169
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)68,2788
Polymers67,2312
Non-polymers1,0476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_444-y-1/2,-x-1/2,-z-1/21
Buried area4310 Å2
ΔGint-4 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.330, 97.330, 124.940
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-403-

SO4

21AaA-661-

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-A1IWF / (5~{S})-5-[[2,6-bis(fluoranyl)phenyl]methoxymethyl]-3-(2-fluorophenyl)-5-methyl-4~{H}-1,2-oxazole


Mass: 335.320 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H16F3NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH4.6, 1.5M ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.38→76.78 Å / Num. obs: 61206 / % possible obs: 99.3 % / Redundancy: 8.2 % / CC1/2: 1 / Rrim(I) all: 0.06 / Net I/σ(I): 17
Reflection shellResolution: 1.38→1.42 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4250 / CC1/2: 0.5 / Rrim(I) all: 1.13 / % possible all: 94

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.38→76.78 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.035 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.06 / ESU R Free: 0.056
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1935 3083 5.037 %
Rwork0.1904 58122 -
all0.191 --
obs-61205 99.285 %
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: 22.402 Å2
Baniso -1Baniso -2Baniso -3
1--0.236 Å20 Å2-0 Å2
2---0.236 Å2-0 Å2
3---0.471 Å2
Refinement stepCycle: LAST / Resolution: 1.38→76.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 35 169 2298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132307
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172124
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.6443151
X-RAY DIFFRACTIONr_angle_other_deg1.5091.5784940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68721.88133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9315416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6791520
X-RAY DIFFRACTIONr_chiral_restr0.0790.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022566
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined0.1990.2398
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.21938
X-RAY DIFFRACTIONr_nbtor_refined0.1690.21072
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21065
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2121
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.221
X-RAY DIFFRACTIONr_nbd_other0.2290.278
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0930.219
X-RAY DIFFRACTIONr_mcbond_it1.7352.1221072
X-RAY DIFFRACTIONr_mcbond_other1.7362.1181071
X-RAY DIFFRACTIONr_mcangle_it2.6063.1781344
X-RAY DIFFRACTIONr_mcangle_other2.6053.1821345
X-RAY DIFFRACTIONr_scbond_it2.7292.481235
X-RAY DIFFRACTIONr_scbond_other2.7322.4821232
X-RAY DIFFRACTIONr_scangle_it4.2393.5871792
X-RAY DIFFRACTIONr_scangle_other4.2433.591787
X-RAY DIFFRACTIONr_lrange_it5.16724.9052571
X-RAY DIFFRACTIONr_lrange_other5.15524.7052551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.38-1.4160.312160.2964033X-RAY DIFFRACTION93.8383
1.416-1.4550.292270.2674046X-RAY DIFFRACTION97.357
1.455-1.4970.2452200.2374052X-RAY DIFFRACTION99.534
1.497-1.5430.2772000.2243915X-RAY DIFFRACTION100
1.543-1.5930.2242010.2043805X-RAY DIFFRACTION99.975
1.593-1.6490.2271970.1963731X-RAY DIFFRACTION99.9491
1.649-1.7120.2191830.1993554X-RAY DIFFRACTION99.8931
1.712-1.7810.1931770.1913455X-RAY DIFFRACTION100
1.781-1.8610.2191820.1893317X-RAY DIFFRACTION100
1.861-1.9510.2131800.1813137X-RAY DIFFRACTION99.9096
1.951-2.0570.1951410.1893041X-RAY DIFFRACTION99.9686
2.057-2.1810.1831630.1792842X-RAY DIFFRACTION99.9667
2.181-2.3320.1921510.1732703X-RAY DIFFRACTION100
2.332-2.5190.1921240.1842524X-RAY DIFFRACTION99.9622
2.519-2.7590.1931250.192319X-RAY DIFFRACTION99.9182
2.759-3.0840.1971170.1982117X-RAY DIFFRACTION99.9553
3.084-3.560.193930.191882X-RAY DIFFRACTION99.8988
3.56-4.3580.152960.1651595X-RAY DIFFRACTION99.9409
4.358-6.1530.149570.1761290X-RAY DIFFRACTION99.9258
6.153-76.780.213330.229765X-RAY DIFFRACTION99.2537

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