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- PDB-8gr8: Crystal structure of peroxisomal citrate synthase (Cit2) from Sac... -

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Basic information

Entry
Database: PDB / ID: 8gr8
TitleCrystal structure of peroxisomal citrate synthase (Cit2) from Saccharomycescerevisiae
ComponentsCitrate synthase
KeywordsTRANSFERASE / glyoxylate cycle / peroxisomal protein / citrate metabolism / SCFUcc1 ubiquitin ligase / proteasome-dependent degradation
Function / homology
Function and homology information


: / 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 / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Citrate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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)104,02613
Polymers102,9522
Non-polymers1,07411
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11040 Å2
ΔGint-76 kcal/mol
Surface area32700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.715, 108.715, 86.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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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 , 5 types, 179 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.5 Å3/Da / Density % sol: 50.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 90 mM KCl, 90 mM HEPES pH 7.5, 13.5% (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 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.39→38.44 Å / Num. obs: 40003 / % possible obs: 99.9 % / Redundancy: 8.4 % / Biso Wilson estimate: 41.48 Å2 / CC1/2: 0.998 / Net I/σ(I): 29.01
Reflection shellResolution: 2.39→2.48 Å / Mean I/σ(I) obs: 6.47 / Num. unique obs: 4001 / CC1/2: 0.926

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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: 2.39→38.44 Å / SU ML: 0.2672 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4668
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2283 3904 4.98 %
Rwork0.1767 74469 -
obs0.1793 39999 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.58 Å2
Refinement stepCycle: LAST / Resolution: 2.39→38.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6920 0 67 168 7155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00197192
X-RAY DIFFRACTIONf_angle_d0.46439727
X-RAY DIFFRACTIONf_chiral_restr0.03651056
X-RAY DIFFRACTIONf_plane_restr0.00361248
X-RAY DIFFRACTIONf_dihedral_angle_d12.07672675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.420.32691400.24382632X-RAY DIFFRACTION99.21
2.42-2.450.33111400.23092648X-RAY DIFFRACTION100
2.45-2.490.28971340.23082690X-RAY DIFFRACTION100
2.49-2.520.28011480.22262665X-RAY DIFFRACTION99.96
2.52-2.560.26381400.23792655X-RAY DIFFRACTION100
2.56-2.590.31441360.22432629X-RAY DIFFRACTION99.96
2.59-2.630.30681410.21542682X-RAY DIFFRACTION99.89
2.63-2.680.26121380.22132676X-RAY DIFFRACTION100
2.68-2.720.28241400.21812646X-RAY DIFFRACTION99.96
2.72-2.770.24551420.21572670X-RAY DIFFRACTION99.96
2.77-2.830.28581400.21612617X-RAY DIFFRACTION100
2.83-2.880.25891400.20482681X-RAY DIFFRACTION99.96
2.88-2.950.2371440.19982683X-RAY DIFFRACTION100
2.95-3.020.27151440.2032686X-RAY DIFFRACTION99.96
3.02-3.090.27261360.21232636X-RAY DIFFRACTION99.93
3.09-3.170.27191400.21572639X-RAY DIFFRACTION100
3.17-3.270.28571300.19942672X-RAY DIFFRACTION100
3.27-3.370.24671440.20212656X-RAY DIFFRACTION100
3.37-3.490.25861340.18712673X-RAY DIFFRACTION100
3.49-3.630.21711400.18242673X-RAY DIFFRACTION100
3.63-3.80.21071440.16562650X-RAY DIFFRACTION100
3.8-40.21331420.16962676X-RAY DIFFRACTION100
4-4.250.23711350.14472632X-RAY DIFFRACTION100
4.25-4.580.15321320.13882683X-RAY DIFFRACTION99.96
4.58-5.040.16081390.13372656X-RAY DIFFRACTION100
5.04-5.760.17911360.16232679X-RAY DIFFRACTION100
5.76-7.250.23381360.16672675X-RAY DIFFRACTION100
7.25-38.440.18831490.13332609X-RAY DIFFRACTION98.92

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