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

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Basic information

Entry
Database: PDB / ID: 9xau
TitleGlyoxysomal Citrate Synthase 3 from Arabidopsis thaliana in complex with OAA
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
OXALOACETATE ION / Citrate synthase 3, peroxisomal
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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
DepositionOct 23, 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
C: Citrate synthase 3, peroxisomal
D: Citrate synthase 3, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,7619
Polymers211,1454
Non-polymers6165
Water7,674426
1
A: Citrate synthase 3, peroxisomal
B: Citrate synthase 3, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,9275
Polymers105,5722
Non-polymers3543
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-60 kcal/mol
Surface area32870 Å2
MethodPISA
2
C: Citrate synthase 3, peroxisomal
D: Citrate synthase 3, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,8344
Polymers105,5722
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13150 Å2
ΔGint-63 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.084, 64.726, 192.512
Angle α, β, γ (deg.)90.000, 92.616, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Citrate synthase 3, peroxisomal


Mass: 52786.164 Da / Num. of mol.: 4
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)
#2: Chemical
ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 426 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM OAA, 65mM HEPES pH 7.0, 6.5mM MgCl2, 13% (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: 1.95→48.1 Å / Num. obs: 141350 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 12.84
Reflection shellResolution: 1.95→1.97 Å / Rmerge(I) obs: 0.435 / Num. unique obs: 4609

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→48.1 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.753 / SU ML: 0.106 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.225 7090 5.016 %
Rwork0.186 134263 -
all0.188 --
obs-141350 99.593 %
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: 44.838 Å2
Baniso -1Baniso -2Baniso -3
1-0.085 Å2-0 Å20.008 Å2
2---0.027 Å2-0 Å2
3----0.059 Å2
Refinement stepCycle: LAST / Resolution: 1.95→48.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13643 0 42 426 14111
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01214011
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613358
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.8319009
X-RAY DIFFRACTIONr_angle_other_deg0.561.75230793
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28151739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.054598
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.679102331
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.99310606
X-RAY DIFFRACTIONr_chiral_restr0.0820.22083
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023141
X-RAY DIFFRACTIONr_nbd_refined0.2210.23223
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.212455
X-RAY DIFFRACTIONr_nbtor_refined0.1850.27049
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.27196
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2553
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0350.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2880.225
X-RAY DIFFRACTIONr_nbd_other0.2780.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.23
X-RAY DIFFRACTIONr_mcbond_it3.9284.3616971
X-RAY DIFFRACTIONr_mcbond_other3.9284.3616971
X-RAY DIFFRACTIONr_mcangle_it5.5997.8258705
X-RAY DIFFRACTIONr_mcangle_other5.5997.8258706
X-RAY DIFFRACTIONr_scbond_it4.4094.8287040
X-RAY DIFFRACTIONr_scbond_other4.4094.8297041
X-RAY DIFFRACTIONr_scangle_it6.6948.66910304
X-RAY DIFFRACTIONr_scangle_other6.6938.66910305
X-RAY DIFFRACTIONr_lrange_it8.80441.7416089
X-RAY DIFFRACTIONr_lrange_other8.80341.7416090
LS refinement shellResolution: 1.95→1.97 Å
RfactorNum. reflection% reflection
Rfree0.3233 226 -
Rwork0.2898 4610 -
obs--97.2 %

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