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- PDB-8gr9: Crystal structure of peroxisomal citrate synthase (Cit2) from Sac... -

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Basic information

Entry
Database: PDB / ID: 8gr9
TitleCrystal structure of peroxisomal citrate synthase (Cit2) from Saccharomyces cerevisiae in complex with oxaloacetate and coenzyme-A
ComponentsCitrate synthase
KeywordsTRANSFERASE / glyoxylate cycle / peroxisomal protein / citrate metabolism / SCFUcc1 ubiquitin ligase / proteasome-dependent degradation
Function / homology
Function and homology information


citrate (Si)-synthase activity / citrate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix
Similarity search - Function
Citrate synthase, eukaryotic-type / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase
Similarity search - Domain/homology
COENZYME A / : / OXALOACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsNishio, K. / Nakatsukasa, K. / Kamura, T. / Mizushima, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H03198 Japan
Japan Society for the Promotion of Science (JSPS)24112009 Japan
CitationJournal: Sci Adv / Year: 2023
Title: Defective import of mitochondrial metabolic enzyme elicits ectopic metabolic stress.
Authors: Nishio, K. / Kawarasaki, T. / Sugiura, Y. / Matsumoto, S. / Konoshima, A. / Takano, Y. / Hayashi, M. / Okumura, F. / Kamura, T. / Mizushima, T. / Nakatsukasa, K.
History
DepositionSep 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,35113
Polymers102,9522
Non-polymers1,39911
Water14,754819
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-89 kcal/mol
Surface area30940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.079, 129.659, 68.127
Angle α, β, γ (deg.)90.000, 116.574, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Citrate synthase


Mass: 51476.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CIT2, GI527_G0000583 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q445

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Non-polymers , 6 types, 830 molecules

#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 819 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 80 mM KCl, 80 mM HEPES pH 7.5, 12% (w/v) PEG 6000

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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: RAYONIX MX300HE / Detector: CCD / Date: Jun 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.48→34.13 Å / Num. obs: 160915 / % possible obs: 99.09 % / Redundancy: 4.3 % / Biso Wilson estimate: 17.45 Å2 / CC1/2: 0.998 / Net I/σ(I): 23.68
Reflection shellResolution: 1.48→1.53 Å / Mean I/σ(I) obs: 4.02 / Num. unique obs: 16181 / CC1/2: 0.838

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.18.2_3874refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→34.13 Å / SU ML: 0.1443 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.751
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1978 3979 1.24 %
Rwork0.178 315976 -
obs0.1782 160885 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.39 Å2
Refinement stepCycle: LAST / Resolution: 1.48→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6868 0 81 819 7768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00367163
X-RAY DIFFRACTIONf_angle_d0.70149716
X-RAY DIFFRACTIONf_chiral_restr0.06641060
X-RAY DIFFRACTIONf_plane_restr0.0041243
X-RAY DIFFRACTIONf_dihedral_angle_d11.36272668
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.490.30481310.290510434X-RAY DIFFRACTION91.39
1.49-1.510.28151610.269211463X-RAY DIFFRACTION99.86
1.51-1.530.30161290.267211325X-RAY DIFFRACTION98.86
1.53-1.550.26341360.248211411X-RAY DIFFRACTION99.83
1.55-1.580.25291460.240911537X-RAY DIFFRACTION99.94
1.58-1.60.2421430.226811348X-RAY DIFFRACTION99.97
1.6-1.620.26481310.22211523X-RAY DIFFRACTION99.93
1.62-1.650.26481510.212211422X-RAY DIFFRACTION99.94
1.65-1.680.20231490.199811416X-RAY DIFFRACTION99.95
1.68-1.710.23091420.196311526X-RAY DIFFRACTION99.95
1.71-1.740.20871410.198211452X-RAY DIFFRACTION99.84
1.74-1.780.22031420.185211355X-RAY DIFFRACTION99.97
1.78-1.820.22691410.189611446X-RAY DIFFRACTION99.97
1.82-1.860.24251550.183711509X-RAY DIFFRACTION99.92
1.86-1.910.2011420.197311384X-RAY DIFFRACTION99.53
1.91-1.960.21411470.192111410X-RAY DIFFRACTION99.42
1.96-2.010.20171460.185311368X-RAY DIFFRACTION99.93
2.01-2.080.24441390.176311420X-RAY DIFFRACTION99.6
2.08-2.150.20361420.179211502X-RAY DIFFRACTION99.97
2.15-2.240.17281480.169711440X-RAY DIFFRACTION99.86
2.24-2.340.18161460.172411384X-RAY DIFFRACTION99.64
2.34-2.470.19651360.170711429X-RAY DIFFRACTION99.96
2.47-2.620.22691520.174911476X-RAY DIFFRACTION99.91
2.62-2.820.17861430.167511423X-RAY DIFFRACTION99.93
2.82-3.110.16261430.166711471X-RAY DIFFRACTION99.92
3.11-3.560.17551410.157311360X-RAY DIFFRACTION99.45
3.56-4.480.16291400.152310701X-RAY DIFFRACTION93.3
4.48-34.130.19121160.17079041X-RAY DIFFRACTION78.94

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