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- PDB-7hrk: PanDDA analysis group deposition -- Crystal Structure of FatA in ... -

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Basic information

Entry
Database: PDB / ID: 7hrk
TitlePanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z89283908
ComponentsOleoyl-acyl carrier protein thioesterase 1, chloroplastic
KeywordsHYDROLASE / SGC - Diamond I04-1 fragment screening / PanDDA / XChemExplorer / fragment screening / XChem / 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
1H-INDOLE-3-CARBOXYLIC ACID / Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.747 Å
AuthorsKot, E. / Ni, X. / Tomlinson, C.W.E. / Fearon, D. / Aschenbrenner, J.C. / Fairhead, M. / Koekemoer, L. / Marx, M.L. / Wright, N.D. / Mulholland, N.P. ...Kot, E. / Ni, X. / Tomlinson, C.W.E. / Fearon, D. / Aschenbrenner, J.C. / Fairhead, M. / Koekemoer, L. / Marx, M.L. / Wright, N.D. / 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: PanDDA analysis group deposition
Authors: Kot, E. / Ni, X. / Tomlinson, C.W.E. / Fearon, D. / Aschenbrenner, J.C. / Fairhead, M. / Koekemoer, L. / Marx, M.L. / Wright, N.D. / Mulholland, N.P. / Montgomery, M.G. / von Delft, F.
History
DepositionDec 23, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2025Provider: repository / Type: Initial release

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


Theoretical massNumber of molelcules
Total (without water)68,06510
Polymers67,2312
Non-polymers8348
Water4,918273
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.420, 99.532, 128.169
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-530-

HOH

21B-529-

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
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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ICO / 1H-INDOLE-3-CARBOXYLIC ACID


Mass: 161.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 2.36 Å3/Da / Density % sol: 47.84 %
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
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92124 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Sep 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.75→49.73 Å / Num. obs: 64130 / % possible obs: 99.6 % / Redundancy: 13.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.05 / Rrim(I) all: 0.186 / Χ2: 0.5 / Net I/σ(I): 9.3 / Num. measured all: 884272
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 98 % / Redundancy: 14 % / Rmerge(I) obs: 4.826 / Num. measured all: 47952 / Num. unique obs: 3414 / CC1/2: 0.359 / Rpim(I) all: 1.323 / Rrim(I) all: 5.006 / Χ2: 0.24 / Net I/σ(I) obs: 0.4

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (23-JAN-2024)refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.747→14.28 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.917 / SU R Cruickshank DPI: 0.139 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.141 / SU Rfree Blow DPI: 0.128 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.2638 3011 4.78 %RANDOM
Rwork0.2395 ---
obs0.2407 62993 97.8 %-
Displacement parametersBiso mean: 37.38 Å2
Baniso -1Baniso -2Baniso -3
1-6.4855 Å20 Å20 Å2
2--3.0539 Å20 Å2
3----9.5394 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å
Refinement stepCycle: LAST / Resolution: 1.747→14.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 47 273 4652
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094601HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.956263HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1656SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes796HARMONIC5
X-RAY DIFFRACTIONt_it4601HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.2
X-RAY DIFFRACTIONt_other_torsion17.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion601SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3661SEMIHARMONIC4
LS refinement shellResolution: 1.75→1.76 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4339 1260 3.02 %
Rwork0.3688 1222 -
all0.3706 1260 -
obs--75.31 %
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)
10.9205-0.35650.04110.4858-0.13060.63770.01390.04560.0335-0.092-0.0410.00740.0319-0.02450.02710.04720.0309-0.0117-0.03760.013-0.0727-19.2621-33.484216.8702
20.5997-0.4185-0.14730.9045-0.00920.7113-0.0548-0.0887-0.00420.04680.02660.0327-0.04330.0270.02830.01460.0320.0097-0.0113-0.0115-0.073-16.182-30.377647.3607
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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