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- PDB-9s4h: Crystal structure of Arabidopsis thaliana Fatty Acid Thioesterase... -

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Basic information

Entry
Database: PDB / ID: 9s4h
TitleCrystal structure of Arabidopsis thaliana Fatty Acid Thioesterase A with the x1816-FU1 ligand
ComponentsOleoyl-acyl carrier protein thioesterase 1, chloroplastic
KeywordsHYDROLASE / Fatty Acid Thioesterase / Plant / Fatty Acid Biosynthesis / Fatty Acid / Chain termination / Dimer / Acyl-ACP thioesterase / Acyl ACP thioesterase / 18:1 FA / FatA / ACP / Herbicide / Mode of Action
Function / homology
Function and homology information


oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / acyl carrier 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: 2.24 Å
AuthorsKot, E. / Ni, X. / Mulholland, N.P. / Montgomery, M.G. / von Delft, F.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research Council United Kingdom
CitationJournal: Pest Manag Sci / Year: 2026
Title: Crystal structure of fatty acid thioesterase A bound by 129 fragments provides diverse development opportunities.
Authors: Kot, E. / Ferla, M.P. / Hollinshead, P.H. / Tomlinson, C.W.E. / Fearon, D. / Aschenbrenner, J.C. / Koekemoer, L. / Winokan, M. / Fairhead, M. / Ni, X. / Chalk, R. / England, K.S. / Varga, L. ...Authors: Kot, E. / Ferla, M.P. / Hollinshead, P.H. / Tomlinson, C.W.E. / Fearon, D. / Aschenbrenner, J.C. / Koekemoer, L. / Winokan, M. / Fairhead, M. / Ni, X. / Chalk, R. / England, K.S. / Varga, L.O. / Montgomery, M.G. / Mulholland, N.P. / von Delft, F.
History
DepositionJul 28, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,8232
Polymers33,6161
Non-polymers2071
Water724
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13570 Å2
Unit cell
Length a, b, c (Å)98.531, 98.531, 128.692
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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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
Details: The N-terminal chloroplast transit peptide (residues 1-74) has been removed. A C-terminal His6 tag was added.
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-A1JLP / 1-(3,5-dihydro-2~{H}-1,4-benzothiazepin-4-yl)ethanone


Mass: 207.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H13NOS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.85 / Details: 0.1M MES pH 6.85, 1.6M Ammonium sulfate

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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 EIGER2 XE 16M / Detector: PIXEL / Date: Jul 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.237→69.77 Å / Num. obs: 7561 / % possible obs: 48.2 % / Redundancy: 22.8 % / CC1/2: 0.967 / Net I/σ(I): 6.4
Reflection shellResolution: 2.237→2.434 Å / Redundancy: 24.9 % / Num. unique obs: 378 / CC1/2: 0.624 / % possible all: 11

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→69.77 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.851 / SU B: 11.159 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.28043 366 4.8 %RANDOM
Rwork0.22739 ---
obs0.23003 7194 48.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.075 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.35 Å20 Å2
3---0.7 Å2
Refinement stepCycle: 1 / Resolution: 2.24→69.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 14 4 2127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122166
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162040
X-RAY DIFFRACTIONr_angle_refined_deg1.3591.8352934
X-RAY DIFFRACTIONr_angle_other_deg0.4541.7864693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7865261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.144519
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.79410385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2331
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022567
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02503
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_it1.6592.5031050
X-RAY DIFFRACTIONr_mcbond_other1.6582.5031050
X-RAY DIFFRACTIONr_mcangle_it2.8644.4821306
X-RAY DIFFRACTIONr_mcangle_other2.8634.4841307
X-RAY DIFFRACTIONr_scbond_it1.7322.7241116
X-RAY DIFFRACTIONr_scbond_other1.7322.7241117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.9684.8991628
X-RAY DIFFRACTIONr_long_range_B_refined4.81823.372350
X-RAY DIFFRACTIONr_long_range_B_other4.81823.372351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.295 Å
RfactorNum. reflection% reflection
Rfree0.003 1 -
Rwork0.277 39 -
obs--3.51 %

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