PDB-9gs1: Crystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (...

ID or keywords:

Entry

Database: PDB / ID: 9gs1

Title

Crystal structure of Arabidopsis thaliana Acyl-ACP Thioesterase (At-FatA) complexed with Oxaziclomefone

Components

Oleoyl-acyl carrier protein thioesterase 1, chloroplastic

Keywords

HYDROLASE / Thioesterase / Herbicide / Inhibitor / Oxaziclomefone

Function / homology

Function and homology information

oleoyl-[acyl-carrier-protein] hydrolase / fatty acyl-[ACP] hydrolase activity / chloroplast / fatty acid biosynthetic process
Similarity search - Function

Biological species

Arabidopsis thaliana (thale cress)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Montgomery, M.G.

Funding support

1items

Citation

Journal: To Be Published
Title: Scaffold-hopping, Bioisosterism and Structure-Based Design in the Development of Novel Acyl-ACP Thioesterase (Fat) Inhibitors as Potential Herbicides
Authors: Croft, R. / Montgomery, M.G.

History

Deposition	Sep 13, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 14, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gs1.cif.gz	123.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9gs1.ent.gz		Display	PDB format
PDBx/mmJSON format	9gs1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gs/9gs1 ftp://data.pdbj.org/pub/pdb/validation_reports/gs/9gs1	HTTPS FTP

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Related structure data

Related structure data	9grrC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1)

Deposited unit

AaA: Oleoyl-acyl carrier protein thioesterase 1, chloroplastic

BaB: Oleoyl-acyl carrier protein thioesterase 1, chloroplastic

hetero molecules

68.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	96.154, 97.839, 126.318
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Components on special symmetry positions

ID	Model	Components
1	1	AaA-581- HOH

Noncrystallographic symmetry (NCS)

NCS domain: (Details: Chains A B)

#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-A1IPE / Oxaziclomefone / 3-[2-[3,5-bis(chloranyl)phenyl]propan-2-yl]-6-methyl-5-phenyl-2~{H}-1,3-oxazin-4-one Mass: 376.276 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₀H₁₉Cl₂NO₂ / 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: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.33 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / Details: 1.6M Ammonium sulphate, 0.1M sodium acetate pH 4.8

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: OTHER / Wavelength: 1.54184 Å
Detector	Type: OXFORD ONYX CCD / Detector: CCD / Date: Dec 15, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 1.9→20.42 Å / Num. obs: 47041 / % possible obs: 99.7 % / Redundancy: 4.2 % / CC_1/2: 0.997 / Net I/σ(I): 11.4
Reflection shell	Resolution: 1.9→1.94 Å / Redundancy: 2.4 % / Num. unique obs: 3102 / CC_1/2: 0.709 / % possible all: 98.7

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0253	refinement
CrysalisPro		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→20.42 Å / Cor.coef. F_o:F_c: 0.934 / Cor.coef. F_o:F_c free: 0.914 / Cross valid method: FREE R-VALUE / ESU R: 0.185 / ESU R Free: 0.166
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2716	2336	4.98 %
R_work	0.2361	44570	-
all	0.238	-	-
obs	-	46906	99.308 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.062 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.28 Å²	0 Å²	0 Å²
2-	-	-2.187 Å²	-0 Å²
3-	-	-	1.907 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→20.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4151	0	66	158	4375

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.013	4341
X-RAY DIFFRACTION	r_bond_other_d	0.035	0.017	3976
X-RAY DIFFRACTION	r_angle_refined_deg	1.52	1.644	5898
X-RAY DIFFRACTION	r_angle_other_deg	2.299	1.579	9207
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.665	5	521
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.853	21.92	250
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.441	15	765
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.044	15	37
X-RAY DIFFRACTION	r_chiral_restr	0.07	0.2	569
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	4825
X-RAY DIFFRACTION	r_gen_planes_other	0.011	0.02	934
X-RAY DIFFRACTION	r_nbd_refined	0.205	0.2	751
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.214	0.2	3626
X-RAY DIFFRACTION	r_nbtor_refined	0.163	0.2	2044
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.074	0.2	1907
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.148	0.2	188
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.079	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.184	0.2	34
X-RAY DIFFRACTION	r_nbd_other	0.232	0.2	100
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.1	0.2	19
X-RAY DIFFRACTION	r_mcbond_it	2.231	2.648	2069
X-RAY DIFFRACTION	r_mcbond_other	2.228	2.648	2068
X-RAY DIFFRACTION	r_mcangle_it	3.311	3.957	2582
X-RAY DIFFRACTION	r_mcangle_other	3.31	3.958	2583
X-RAY DIFFRACTION	r_scbond_it	3.018	3.069	2271
X-RAY DIFFRACTION	r_scbond_other	3.018	3.069	2272
X-RAY DIFFRACTION	r_scangle_it	4.689	4.444	3311
X-RAY DIFFRACTION	r_scangle_other	4.688	4.444	3312
X-RAY DIFFRACTION	r_lrange_it	6.486	30.746	4759
X-RAY DIFFRACTION	r_lrange_other	6.485	30.749	4760
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.09	0.05	8083

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.949	0.359	191	0.316	3211	X-RAY DIFFRACTION	98.5801
1.949-2.003	0.303	174	0.284	3140	X-RAY DIFFRACTION	98.9845
2.003-2.061	0.304	166	0.28	3106	X-RAY DIFFRACTION	99.1215
2.061-2.124	0.316	151	0.276	3010	X-RAY DIFFRACTION	99.9368
2.124-2.194	0.275	151	0.264	2931	X-RAY DIFFRACTION	99.9028
2.194-2.271	0.305	145	0.26	2854	X-RAY DIFFRACTION	99.8003
2.271-2.356	0.34	146	0.239	2723	X-RAY DIFFRACTION	99.826
2.356-2.452	0.319	114	0.249	2683	X-RAY DIFFRACTION	99.8216
2.452-2.561	0.357	135	0.264	2497	X-RAY DIFFRACTION	99.6592
2.561-2.686	0.309	125	0.259	2429	X-RAY DIFFRACTION	99.6488
2.686-2.831	0.294	126	0.249	2317	X-RAY DIFFRACTION	99.2686
2.831-3.003	0.219	115	0.241	2168	X-RAY DIFFRACTION	99.304
3.003-3.21	0.296	95	0.243	2072	X-RAY DIFFRACTION	99.4949
3.21-3.466	0.228	94	0.217	1921	X-RAY DIFFRACTION	99.408
3.466-3.797	0.228	96	0.205	1749	X-RAY DIFFRACTION	99.0338
3.797-4.243	0.218	100	0.203	1596	X-RAY DIFFRACTION	98.7194
4.243-4.897	0.233	69	0.178	1446	X-RAY DIFFRACTION	99.4094
4.897-5.992	0.25	61	0.217	1218	X-RAY DIFFRACTION	99.8439
5.992-8.449	0.301	52	0.232	978	X-RAY DIFFRACTION	100
8.449-20.42	0.237	30	0.238	521	X-RAY DIFFRACTION	90.4762

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