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- PDB-8zvw: human citrate synthase complexed with oxaloacetate and coenzyme A -

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Basic information

Entry
Database: PDB / ID: 8zvw
Titlehuman citrate synthase complexed with oxaloacetate and coenzyme A
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
COENZYME A / OXALOACETATE ION / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 oxaloacetate and coenzyme A
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5313
Polymers48,6331
Non-polymers8992
Water1,72996
1
A: Citrate synthase, mitochondrial
hetero molecules

A: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,0626
Polymers97,2652
Non-polymers1,7974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area11760 Å2
ΔGint-59 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.370, 57.370, 250.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-667-

HOH

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Components

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


Mass: 48632.547 Da / Num. of mol.: 1
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.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.12 Å3/Da / Density % sol: 42 %
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: Oct 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.82→29.1 Å / Num. obs: 38983 / % possible obs: 100 % / Redundancy: 22.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.232 / Net I/σ(I): 8.8
Reflection shellResolution: 1.82→1.87 Å / Rmerge(I) obs: 2.068 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2830 / CC1/2: 0.348 / Rrim(I) all: 2.128

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→29.1 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.065 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29798 1876 4.8 %RANDOM
Rwork0.2225 ---
obs0.22603 36998 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0 Å2-0 Å2
2---0.31 Å2-0 Å2
3---0.62 Å2
Refinement stepCycle: 1 / Resolution: 1.82→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3470 0 0 96 3566
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123568
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163349
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.8314851
X-RAY DIFFRACTIONr_angle_other_deg0.5691.7477718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.238522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.66810593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02809
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_it4.2344.3541737
X-RAY DIFFRACTIONr_mcbond_other4.2284.3541737
X-RAY DIFFRACTIONr_mcangle_it5.6577.8192170
X-RAY DIFFRACTIONr_mcangle_other5.6577.822171
X-RAY DIFFRACTIONr_scbond_it4.7774.9091831
X-RAY DIFFRACTIONr_scbond_other4.7764.9111832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9478.8272681
X-RAY DIFFRACTIONr_long_range_B_refined10.23247.954389
X-RAY DIFFRACTIONr_long_range_B_other10.23547.774384
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.82→1.867 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 137 -
Rwork0.365 2678 -
obs--100 %

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