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- PDB-7hu5: PanDDA analysis group deposition -- Crystal Structure of FatA in ... -

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Basic information

Entry
Database: PDB / ID: 7hu5
TitlePanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z768399682
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
: / Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 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)67,6864
Polymers67,2312
Non-polymers4552
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.343, 99.440, 128.137
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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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-A1BFX / [(2R,5S)-2,5-dimethylmorpholin-4-yl](1,2,5-thiadiazol-3-yl)methanone


Mass: 227.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C9H13N3O2S / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.35 Å3/Da / Density % sol: 47.74 %
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: Oct 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.22→78.54 Å / Num. obs: 31712 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.546 / Rpim(I) all: 0.154 / Rrim(I) all: 0.567 / Χ2: 0.37 / Net I/σ(I): 5.3 / Num. measured all: 428504
Reflection shellResolution: 2.22→2.29 Å / % possible obs: 99.3 % / Redundancy: 13.7 % / Rmerge(I) obs: 5.626 / Num. measured all: 39416 / Num. unique obs: 2873 / CC1/2: 0.882 / Rpim(I) all: 1.572 / Rrim(I) all: 5.844 / Χ2: 0.47 / Net I/σ(I) obs: 0.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→78.56 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.805 / SU B: 30.825 / SU ML: 0.643 / Cross valid method: THROUGHOUT / ESU R Free: 0.475 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37674 1484 4.9 %RANDOM
Rwork0.31472 ---
obs0.31783 28602 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0 Å20 Å2
2---0.68 Å2-0 Å2
3---0.77 Å2
Refinement stepCycle: 1 / Resolution: 2.22→78.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4260 0 30 15 4305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01612893
X-RAY DIFFRACTIONr_bond_other_d0.0010.0147133
X-RAY DIFFRACTIONr_angle_refined_deg1.2451.65110728
X-RAY DIFFRACTIONr_angle_other_deg1.0681.58616445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.53120.637471
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.083151377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.311578
X-RAY DIFFRACTIONr_chiral_restr0.0390.21023
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029146
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021962
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_it2.0946.6416546
X-RAY DIFFRACTIONr_mcbond_other2.2687.0155579
X-RAY DIFFRACTIONr_mcangle_it4.9579.7054766
X-RAY DIFFRACTIONr_mcangle_other4.9579.7064767
X-RAY DIFFRACTIONr_scbond_it1.5757.1156347
X-RAY DIFFRACTIONr_scbond_other1.5877.0546225
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.6069.9155891
X-RAY DIFFRACTIONr_long_range_B_refined16.24474.2769505
X-RAY DIFFRACTIONr_long_range_B_other15.81374.5979331
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.752 91 -
Rwork0.736 2101 -
obs--95.06 %

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