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

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Basic information

Entry
Database: PDB / ID: 9hrq
TitleCrystal structure of Arabidopsis thaliana Fatty Acid Thioesterase A with an unidentified ligand which closes the N-terminal domain
ComponentsOleoyl-acyl carrier protein thioesterase 1, chloroplastic
KeywordsHYDROLASE / 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 / 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
Unknown ligand / Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKot, E. / Ni, X. / Koekemoer, L. / 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: To Be Published
Title: Crystal structure of Arabidopsis thaliana Fatty Acid Thioesterase A with an unidentified ligand which closes the N-terminal domain
Authors: Kot, E. / Ni, X. / Koekemoer, L. / Mulholland, N.P. / Montgomery, M.G. / von Delft, F.
History
DepositionDec 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,3454
Polymers67,2312
Non-polymers1142
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-14 kcal/mol
Surface area23990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.790, 98.580, 128.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-511-

HOH

21B-573-

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.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Mass: 18.015 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 45.93 %
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: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.54→49.29 Å / Num. obs: 90324 / % possible obs: 99.7 % / Redundancy: 26.2 % / CC1/2: 1 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.023 / Rrim(I) all: 0.12 / Χ2: 1.02 / Net I/σ(I): 17.4 / Num. measured all: 2368183
Reflection shellResolution: 1.54→1.58 Å / % possible obs: 97.1 % / Redundancy: 15.2 % / Rmerge(I) obs: 3.12 / Num. measured all: 97727 / Num. unique obs: 6419 / CC1/2: 0.356 / Rpim(I) all: 0.787 / Rrim(I) all: 3.225 / Χ2: 0.95 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→49.29 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.693 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. AN UNIDENTIFIED LIGAND, DESIGNATED UNL, HAS BEEN MODELLED IN CHAIN B NEAR ARG176.
RfactorNum. reflection% reflectionSelection details
Rfree0.2175 4539 5 %RANDOM
Rwork0.1889 ---
obs0.19033 85783 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.551 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-0 Å2
2---0.34 Å20 Å2
3---0.84 Å2
Refinement stepCycle: 1 / Resolution: 1.54→49.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4277 0 23 421 4721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0124409
X-RAY DIFFRACTIONr_bond_other_d0.0020.0164160
X-RAY DIFFRACTIONr_angle_refined_deg1.791.8345980
X-RAY DIFFRACTIONr_angle_other_deg0.6341.799565
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.806539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.37410797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025284
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021040
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_it2.072.3182140
X-RAY DIFFRACTIONr_mcbond_other2.072.3182140
X-RAY DIFFRACTIONr_mcangle_it2.9024.152673
X-RAY DIFFRACTIONr_mcangle_other2.9024.1522674
X-RAY DIFFRACTIONr_scbond_it3.9082.7982269
X-RAY DIFFRACTIONr_scbond_other3.9012.7972266
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9224.9073299
X-RAY DIFFRACTIONr_long_range_B_refined6.98624.574927
X-RAY DIFFRACTIONr_long_range_B_other6.96924.324794
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.54→1.58 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 357 -
Rwork0.315 6053 -
obs--96.9 %

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