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

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Basic information

Entry
Database: PDB / ID: 7hsn
TitlePanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z2217052426
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: 2.73 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)67,6424
Polymers67,2312
Non-polymers4112
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.960, 98.990, 128.280
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-A1BMR / (2S,3R)-1-benzyl-2-methylpiperidin-3-ol


Mass: 205.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19NO / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
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 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.73→78.35 Å / Num. obs: 17107 / % possible obs: 100 % / Redundancy: 13.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.127 / Rrim(I) all: 0.467 / Χ2: 1 / Net I/σ(I): 5.6 / Num. measured all: 229715
Reflection shellResolution: 2.73→2.8 Å / % possible obs: 100 % / Redundancy: 13.8 % / Rmerge(I) obs: 4.888 / Num. measured all: 17263 / Num. unique obs: 1252 / CC1/2: 0.335 / Rpim(I) all: 1.359 / Rrim(I) all: 5.075 / Χ2: 0.92 / Net I/σ(I) obs: 0.6

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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: 2.73→24.84 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.857 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.422
RfactorNum. reflection% reflectionSelection details
Rfree0.304 834 4.89 %RANDOM
Rwork0.2507 ---
obs0.2535 17064 99.9 %-
Displacement parametersBiso mean: 62 Å2
Baniso -1Baniso -2Baniso -3
1-3.3211 Å20 Å20 Å2
2--1.5115 Å20 Å2
3----4.8326 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: LAST / Resolution: 2.73→24.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4272 0 30 118 4420
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0064472HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.86067HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1627SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes766HARMONIC5
X-RAY DIFFRACTIONt_it4472HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.31
X-RAY DIFFRACTIONt_other_torsion18.95
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion591SEMIHARMONIC5
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_contact3282SEMIHARMONIC4
LS refinement shellResolution: 2.73→2.75 Å / Total num. of bins used: 42
RfactorNum. reflection% reflection
Rfree0.6894 417 4.08 %
Rwork0.3443 400 -
all0.3567 417 -
obs--98.1 %
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)
12.4901-0.63140.08010.8630.11861.10790.01240.2008-0.00120.0277-0.05030.0485-0.03890.05050.0378-0.10550.04050.0113-0.09650.0269-0.1223-19.012-33.106416.8403
20.8081-0.45610.01082.06060.12740.9253-0.04350.02580.01590.2030.04110.06530.0662-0.02870.0024-0.10610.04780.022-0.07870.0116-0.1439-16.2853-30.465247.4141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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