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- PDB-8gqz: Crystal structure of mitochondrial citrate synthase (Cit1) from S... -

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Basic information

Entry
Database: PDB / ID: 8gqz
TitleCrystal structure of mitochondrial citrate synthase (Cit1) from Saccharomyces cerevisiae
ComponentsCitrate synthase
KeywordsTRANSFERASE / TCA cycle / mitochondrial protein / citrate metabolism / SCFUcc1 ubiquitin ligase / proteasome-dependent degradation
Function / homology
Function and homology information


: / citrate metabolic process / tricarboxylic acid cycle
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
ACETATE ION / Citrate synthase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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
DepositionAug 31, 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)107,24110
Polymers106,8662
Non-polymers3758
Water17,060947
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10040 Å2
ΔGint-126 kcal/mol
Surface area33170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.328, 102.398, 146.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Citrate synthase


Mass: 53432.906 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CIT1, GI527_G0005109 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5Q7J3

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Non-polymers , 5 types, 955 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 947 / 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: 2.19 Å3/Da / Density % sol: 43.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 140 mM Ca(OAc)2, 70 mM Tris pH 7.0, 14% (w/v) PEG 3000

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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: Jul 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.42→31.64 Å / Num. obs: 173510 / % possible obs: 97.91 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.8 Å2 / CC1/2: 0.998 / Net I/σ(I): 26.36
Reflection shellResolution: 1.42→1.471 Å / Num. unique obs: 16335 / CC1/2: 0.897

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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: 1.42→31.64 Å / SU ML: 0.1418 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.3746
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1969 3821 1.16 %
Rwork0.1663 326176 -
obs0.1666 173475 96.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.83 Å2
Refinement stepCycle: LAST / Resolution: 1.42→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6916 0 19 947 7882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01877236
X-RAY DIFFRACTIONf_angle_d1.55079821
X-RAY DIFFRACTIONf_chiral_restr0.11621082
X-RAY DIFFRACTIONf_plane_restr0.0111259
X-RAY DIFFRACTIONf_dihedral_angle_d13.12972712
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.42-1.440.28691310.274111311X-RAY DIFFRACTION90.23
1.44-1.460.31511300.264711510X-RAY DIFFRACTION91.6
1.46-1.480.26311310.250311455X-RAY DIFFRACTION91.59
1.48-1.50.32341410.237811580X-RAY DIFFRACTION92.37
1.5-1.520.31721370.227211618X-RAY DIFFRACTION92.38
1.52-1.540.25081350.22411604X-RAY DIFFRACTION92.88
1.54-1.570.26751360.214411742X-RAY DIFFRACTION93.7
1.57-1.60.29121380.203311930X-RAY DIFFRACTION94.2
1.6-1.630.22281350.196511820X-RAY DIFFRACTION94.92
1.63-1.660.19571430.191611952X-RAY DIFFRACTION95.6
1.66-1.690.21591410.19112152X-RAY DIFFRACTION96.34
1.69-1.730.23041420.183812145X-RAY DIFFRACTION97.02
1.73-1.770.22051420.180512204X-RAY DIFFRACTION97.54
1.77-1.810.20681480.180312337X-RAY DIFFRACTION98.08
1.81-1.860.20891480.185212351X-RAY DIFFRACTION98.64
1.86-1.920.27591450.178312379X-RAY DIFFRACTION99.01
1.92-1.980.21041460.173112443X-RAY DIFFRACTION99.35
1.98-2.050.21490.172312508X-RAY DIFFRACTION99.6
2.05-2.130.18551470.160812524X-RAY DIFFRACTION99.73
2.13-2.230.25291440.155812540X-RAY DIFFRACTION99.76
2.23-2.340.15351470.159812515X-RAY DIFFRACTION99.91
2.34-2.490.19081500.162112535X-RAY DIFFRACTION99.91
2.49-2.680.18761470.155612484X-RAY DIFFRACTION99.91
2.68-2.950.17721430.156912542X-RAY DIFFRACTION99.87
2.95-3.380.18081500.146712506X-RAY DIFFRACTION99.87
3.38-4.260.16391440.135612275X-RAY DIFFRACTION97.89
4.26-31.640.14911310.149911214X-RAY DIFFRACTION89.42

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