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- PDB-9x0i: Glyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in compl... -

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Basic information

Entry
Database: PDB / ID: 9x0i
TitleGlyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA and CoA
ComponentsCitrate synthase 3, peroxisomal
KeywordsTRANSFERASE / citrate synthase / glyoxysome / glyoxylate cycle / Arabidopsis
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate synthase activity / fatty acid beta-oxidation / tricarboxylic acid cycle / peroxisome / carbohydrate metabolic process / mitochondrial matrix / cytosol
Similarity search - Function
Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain
Similarity search - Domain/homology
COENZYME A / OXALOACETATE ION / DI(HYDROXYETHYL)ETHER / Citrate synthase 3, peroxisomal
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsNishio, K. / Takagi, K. / Mizushima, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K01968 Japan
CitationJournal: J.Struct.Biol. / Year: 2026
Title: Crystal structure of glyoxysomal citrate synthase 3 from Arabidopsis thaliana reveals a novel oligomeric state.
Authors: Nishio, K. / Takagi, K. / Mizushima, T.
History
DepositionSep 30, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrate synthase 3, peroxisomal
B: Citrate synthase 3, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,00415
Polymers105,5722
Non-polymers2,43113
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16350 Å2
ΔGint-77 kcal/mol
Surface area33200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)193.859, 60.597, 76.864
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-796-

HOH

21A-1141-

HOH

31B-879-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Citrate synthase 3, peroxisomal


Mass: 52786.164 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CSY3, At2g42790, F7D19.21 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9SJH7, citrate synthase (unknown stereospecificity)

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Non-polymers , 7 types, 800 molecules

#2: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.01 Å3/Da / Density % sol: 38.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20mM CoA and 20mM OAA in 90mM HEPES pH7.0, 9mM MgCl2, 18%(w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→38.32 Å / Num. obs: 100323 / % possible obs: 98.6 % / Redundancy: 6.7 % / CC1/2: 0.999 / Net I/σ(I): 17.1
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 7005 / CC1/2: 0.926

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→38.32 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.897 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.095 / ESU R Free: 0.095
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1967 1977 1.996 %
Rwork0.1659 97085 -
all0.159 --
obs-99058 98.63 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.547 Å2-0 Å20 Å2
2--0.791 Å2-0 Å2
3---0.757 Å2
Refinement stepCycle: LAST / Resolution: 1.7→38.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6892 0 152 787 7831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0127285
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166960
X-RAY DIFFRACTIONr_angle_refined_deg1.881.8349904
X-RAY DIFFRACTIONr_angle_other_deg0.6421.75116064
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1355902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.342556
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.06552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.989101214
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.3110307
X-RAY DIFFRACTIONr_chiral_restr0.0960.21088
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028456
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021618
X-RAY DIFFRACTIONr_nbd_refined0.2250.21697
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.26724
X-RAY DIFFRACTIONr_nbtor_refined0.1880.23693
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.23849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2667
X-RAY DIFFRACTIONr_metal_ion_refined0.1390.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.223
X-RAY DIFFRACTIONr_nbd_other0.1910.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2060.247
X-RAY DIFFRACTIONr_mcbond_it2.8052.5923549
X-RAY DIFFRACTIONr_mcbond_other2.8012.5923549
X-RAY DIFFRACTIONr_mcangle_it3.9734.6494440
X-RAY DIFFRACTIONr_mcangle_other3.9744.654441
X-RAY DIFFRACTIONr_scbond_it3.9743.113736
X-RAY DIFFRACTIONr_scbond_other3.9453.1083734
X-RAY DIFFRACTIONr_scangle_it5.9815.515453
X-RAY DIFFRACTIONr_scangle_other5.985.5115454
X-RAY DIFFRACTIONr_lrange_it7.53128.9248833
X-RAY DIFFRACTIONr_lrange_other7.53128.9278834
LS refinement shellResolution: 1.7→1.74 Å
RfactorNum. reflection% reflection
Rfree0.2586 133 -
Rwork0.2339 6674 -
obs--99.6374 %

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