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- PDB-7hu4: PanDDA analysis group deposition -- Crystal Structure of FatA in ... -

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Basic information

Entry
Database: PDB / ID: 7hu4
TitlePanDDA analysis group deposition -- Crystal Structure of FatA in complex with Z760048004
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
N-(6-methylpyridin-2-yl)-L-prolinamide / Oleoyl-acyl carrier protein thioesterase 1, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.104 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)67,8346
Polymers67,2312
Non-polymers6034
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.476, 98.442, 128.167
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-545-

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-WN4 / N-(6-methylpyridin-2-yl)-L-prolinamide


Mass: 205.256 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H15N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.31 Å3/Da / Density % sol: 46.75 %
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 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92124 Å / Relative weight: 1
ReflectionResolution: 2.1→78.08 Å / Num. obs: 36409 / % possible obs: 99.7 % / Redundancy: 13.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.303 / Rpim(I) all: 0.085 / Rrim(I) all: 0.315 / Χ2: 0.36 / Net I/σ(I): 5.2 / Num. measured all: 493167
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 96.1 % / Redundancy: 14.1 % / Rmerge(I) obs: 5.605 / Num. measured all: 39449 / Num. unique obs: 2803 / CC1/2: 0.314 / Rpim(I) all: 1.535 / Rrim(I) all: 5.814 / Χ2: 0.2 / Net I/σ(I) obs: 0.3

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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: 2.104→28.01 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.846 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.311 / SU Rfree Blow DPI: 0.248 / SU Rfree Cruickshank DPI: 0.25
RfactorNum. reflection% reflectionSelection details
Rfree0.3306 1713 4.81 %RANDOM
Rwork0.2858 ---
obs0.288 35617 97.7 %-
Displacement parametersBiso mean: 58.61 Å2
Baniso -1Baniso -2Baniso -3
1-10.6318 Å20 Å20 Å2
2--12.0326 Å20 Å2
3----22.6645 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.104→28.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4266 0 40 148 4454
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0064518HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.86139HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1645SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes777HARMONIC5
X-RAY DIFFRACTIONt_it4518HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.47
X-RAY DIFFRACTIONt_other_torsion18.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion592SEMIHARMONIC5
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_contact3345SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.13 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.4715 713 3.23 %
Rwork0.478 690 -
all0.4778 713 -
obs--55.34 %
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)
13.2473-0.83040.32761.1310.09831.1172-0.00370.0541-0.0414-0.06830.0072-0.0098-0.0212-0.0147-0.0035-0.0880.04690.02510.04380.0231-0.1876-19.0491-32.954616.7286
20.7106-0.19450.17922.26260.16020.8820.0013-0.0628-0.08330.055-0.00950.115-0.0055-0.00380.0082-0.12530.06020.03690.15110.0318-0.213-16.4693-30.462947.492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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