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

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Basic information

Entry
Database: PDB / ID: 7hrg
TitlePanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z104474062
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
3-chlorobenzoate / Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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)67,9298
Polymers67,2312
Non-polymers6976
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.595, 99.614, 127.835
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-561-

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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-3BZ / 3-chlorobenzoate


Mass: 156.566 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C7H5ClO2 / Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Production host: Escherichia coli (E. coli) / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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 11, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 1.92→78.59 Å / Num. obs: 48653 / % possible obs: 99.6 % / Redundancy: 13.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.05 / Rrim(I) all: 0.183 / Χ2: 0.45 / Net I/σ(I): 8.4 / Num. measured all: 660207
Reflection shellResolution: 1.92→1.96 Å / % possible obs: 97.8 % / Redundancy: 13.8 % / Rmerge(I) obs: 1.076 / Num. measured all: 43814 / Num. unique obs: 3173 / CC1/2: 0.938 / Rpim(I) all: 0.3 / Rrim(I) all: 1.117 / Χ2: 0.48 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
REFMAC5refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→78.58 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.856 / SU B: 25.643 / SU ML: 0.664 / Cross valid method: THROUGHOUT / ESU R Free: 0.456 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.37008 2253 4.8 %RANDOM
Rwork0.32277 ---
obs0.3251 44212 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.211 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å2-0 Å2
2---0.03 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.92→78.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4302 0 40 130 4472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01635187
X-RAY DIFFRACTIONr_bond_other_d0.0010.01515849
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.64824049
X-RAY DIFFRACTIONr_angle_other_deg1.0881.59736944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.11352453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33622.3441045
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.347153262
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.20415158
X-RAY DIFFRACTIONr_chiral_restr0.0490.22184
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0222093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024391
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_it1.6315.30317409
X-RAY DIFFRACTIONr_mcbond_other1.6475.33317018
X-RAY DIFFRACTIONr_mcangle_it3.6637.80711395
X-RAY DIFFRACTIONr_mcangle_other3.6637.80711396
X-RAY DIFFRACTIONr_scbond_it1.715.6317778
X-RAY DIFFRACTIONr_scbond_other1.7055.63917563
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7748.23912508
X-RAY DIFFRACTIONr_long_range_B_refined7.47559.28319153
X-RAY DIFFRACTIONr_long_range_B_other7.44659.28619094
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.919→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.776 129 -
Rwork0.811 2603 -
obs--76.31 %

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