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- PDB-8zvv: human citrate synthase complexed with citrate -

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Basic information

Entry
Database: PDB / ID: 8zvv
Titlehuman citrate synthase complexed with citrate
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
CITRIC ACID / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 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 synthase complexed with citrate
Authors: Yang, L.Y. / Fang, Y.J.
History
DepositionJun 12, 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
B: Citrate synthase, mitochondrial
C: Citrate synthase, mitochondrial
D: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,2998
Polymers194,5304
Non-polymers7684
Water15,403855
1
A: Citrate synthase, mitochondrial
B: Citrate synthase, mitochondrial
C: Citrate synthase, mitochondrial
D: Citrate synthase, mitochondrial
hetero molecules

A: Citrate synthase, mitochondrial
B: Citrate synthase, mitochondrial
C: Citrate synthase, mitochondrial
D: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)390,59716
Polymers389,0608
Non-polymers1,5378
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area10270 Å2
ΔGint-57 kcal/mol
Surface area30050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.548, 194.332, 69.369
Angle α, β, γ (deg.)90.00, 90.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 48632.547 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-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 1.99 Å3/Da / Density % sol: 38.31 %
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: Dec 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.59→97.17 Å / Num. obs: 201557 / % possible obs: 99.1 % / Redundancy: 4.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.134 / Rrim(I) all: 0.15 / Net I/σ(I): 6.5
Reflection shellResolution: 1.59→1.68 Å / Rmerge(I) obs: 1.272 / Num. unique obs: 28976 / CC1/2: 0.323 / Rrim(I) all: 1.456

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Processing

Software
NameVersionClassification
REFMAC5.8.0411refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.59→97.17 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.907 / SU B: 4.957 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29543 10100 5 %RANDOM
Rwork0.24144 ---
obs0.24419 191015 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å2-0.96 Å2
2--2.76 Å20 Å2
3----1.83 Å2
Refinement stepCycle: 1 / Resolution: 1.59→97.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13728 0 0 855 14583
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01214088
X-RAY DIFFRACTIONr_bond_other_d0.0010.01613288
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.64619132
X-RAY DIFFRACTIONr_angle_other_deg0.491.56930620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.16151740
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.286576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.986102372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0720.22100
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216356
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_it2.462.9116948
X-RAY DIFFRACTIONr_mcbond_other2.4592.9116948
X-RAY DIFFRACTIONr_mcangle_it3.6215.2298680
X-RAY DIFFRACTIONr_mcangle_other3.6215.2298681
X-RAY DIFFRACTIONr_scbond_it2.8183.1927140
X-RAY DIFFRACTIONr_scbond_other2.8163.1927137
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2795.72110449
X-RAY DIFFRACTIONr_long_range_B_refined8.36436.8918353
X-RAY DIFFRACTIONr_long_range_B_other8.32136.4918253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.59→1.631 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.462 676 -
Rwork0.428 13670 -
obs--95.57 %

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