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- PDB-8zvl: human citrate synthases complexed with oxaloacetate -

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Basic information

Entry
Database: PDB / ID: 8zvl
Titlehuman citrate synthases complexed with oxaloacetate
ComponentsCitrate synthase, mitochondrial
KeywordsTRANSFERASE / citrate synthase / complex
Function / homology
Function and homology information


citrate (Si)-synthase / Citric acid cycle (TCA cycle) / : / citrate metabolic process / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / carbohydrate metabolic process / mitochondrial matrix ...citrate (Si)-synthase / Citric acid cycle (TCA cycle) / : / citrate metabolic process / Maturation of TCA enzymes and regulation of TCA cycle / Mitochondrial protein import / tricarboxylic acid cycle / Mitochondrial protein degradation / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / RNA binding / extracellular exosome / identical protein binding / nucleus
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
OXALOACETATE ION / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsYang, L.Y. / Fang, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: human citrate synthases complexed with oxaloacetate
Authors: Yang, L.Y. / Fang, Y.J.
History
DepositionJun 11, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 18, 2025Provider: 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, mitochondrial
D: Citrate synthase, mitochondrial
B: Citrate synthase, mitochondrial
C: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,4407
Polymers195,0474
Non-polymers3933
Water9,998555
1
A: Citrate synthase, mitochondrial
D: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,7864
Polymers97,5232
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-63 kcal/mol
Surface area30930 Å2
MethodPISA
2
B: Citrate synthase, mitochondrial
C: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,6553
Polymers97,5232
Non-polymers1311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-62 kcal/mol
Surface area30330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.600, 78.010, 103.120
Angle α, β, γ (deg.)70.75, 81.37, 74.74
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Citrate synthase, mitochondrial / Citrate (Si)-synthase


Mass: 48761.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CS / Production host: Escherichia coli (E. coli) / References: UniProt: O75390, citrate (Si)-synthase
#2: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H3O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium acetate pH=7.1, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→32.68 Å / Num. obs: 98576 / % possible obs: 96.4 % / Redundancy: 3.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.151 / Rrim(I) all: 0.181 / Net I/σ(I): 5.7
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 0.828 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 7191 / CC1/2: 0.423 / Rrim(I) all: 1.012

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→32.68 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.405 / SU ML: 0.169 / Cross valid method: THROUGHOUT / ESU R: 0.255 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25837 4896 5 %RANDOM
Rwork0.1935 ---
obs0.19669 93672 96.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0.03 Å20 Å2
2---0.01 Å20.03 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.05→32.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13692 0 27 555 14274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01214068
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613286
X-RAY DIFFRACTIONr_angle_refined_deg1.7771.82919096
X-RAY DIFFRACTIONr_angle_other_deg0.5991.74930609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55651738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.324579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.597102378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0860.22096
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216560
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023212
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0033.9196952
X-RAY DIFFRACTIONr_mcbond_other3.9973.9196952
X-RAY DIFFRACTIONr_mcangle_it5.637.0318684
X-RAY DIFFRACTIONr_mcangle_other5.637.0318685
X-RAY DIFFRACTIONr_scbond_it4.8164.477116
X-RAY DIFFRACTIONr_scbond_other4.8164.477117
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2277.9510411
X-RAY DIFFRACTIONr_long_range_B_refined10.0342.1616636
X-RAY DIFFRACTIONr_long_range_B_other10.03342.0616576
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 355 -
Rwork0.305 6806 -
obs--95.89 %

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