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- PDB-8zvt: Human citrate synthase intermediate 3 -

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Basic information

Entry
Database: PDB / ID: 8zvt
TitleHuman citrate synthase intermediate 3
ComponentsCitrate synthase, mitochondrial
KeywordsTRANSFERASE / citrate synthase / complex / reaction intermediate
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
ACETIC ACID / COENZYME A / 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 synthase intermediate 3
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)49,7494
Polymers48,7911
Non-polymers9593
Water2,738152
1
A: Citrate synthase, mitochondrial
hetero molecules

A: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,4998
Polymers97,5812
Non-polymers1,9176
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area11640 Å2
ΔGint-58 kcal/mol
Surface area30240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.840, 57.840, 250.360
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-712-

HOH

21A-721-

HOH

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Components

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


Mass: 48790.703 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-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical ChemComp-COA / COENZYME A


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


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.15 Å3/Da / Density % sol: 42.68 %
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: 2.05→31.68 Å / Num. obs: 27927 / % possible obs: 99.9 % / Redundancy: 24.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.262 / Rrim(I) all: 0.268 / Net I/σ(I): 12.6
Reflection shellResolution: 2.05→2.1 Å / Rmerge(I) obs: 1.586 / Num. unique obs: 2004 / CC1/2: 0.754 / Rrim(I) all: 1.617

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→31.68 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.898 / SU B: 5.421 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26936 1362 4.9 %RANDOM
Rwork0.20089 ---
obs0.20399 26468 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.05→31.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 48 152 3630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123571
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163352
X-RAY DIFFRACTIONr_angle_refined_deg1.631.8314854
X-RAY DIFFRACTIONr_angle_other_deg0.5491.7477724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5985435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.896522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50910593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2533
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024174
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_it2.7993.2221738
X-RAY DIFFRACTIONr_mcbond_other2.7983.2211737
X-RAY DIFFRACTIONr_mcangle_it4.0275.7822170
X-RAY DIFFRACTIONr_mcangle_other4.0265.7842171
X-RAY DIFFRACTIONr_scbond_it3.3723.6551833
X-RAY DIFFRACTIONr_scbond_other3.3723.6561834
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2256.5392684
X-RAY DIFFRACTIONr_long_range_B_refined6.77132.854273
X-RAY DIFFRACTIONr_long_range_B_other6.76832.734256
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
Rfree0.284 127 -
Rwork0.276 1870 -
obs--100 %

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