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- PDB-8zvm: Human citrate synthase intermediate 1 -

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Basic information

Entry
Database: PDB / ID: 8zvm
TitleHuman citrate synthase intermediate 1
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
ACETYL GROUP / COENZYME A / OXALOACETATE ION / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 1
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
B: Citrate synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2085
Polymers97,2652
Non-polymers9433
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9130 Å2
ΔGint-66 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.213, 59.819, 73.241
Angle α, β, γ (deg.)101.72, 98.66, 116.55
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 48632.547 Da / Num. of mol.: 2
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-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#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.: 122 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
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: 1.97→68.94 Å / Num. obs: 35465 / % possible obs: 84.6 % / Redundancy: 2 % / CC1/2: 0.981 / Rmerge(I) obs: 0.115 / Rrim(I) all: 0.149 / Net I/σ(I): 2.9
Reflection shellResolution: 1.97→2.17 Å / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1773 / CC1/2: 0.309 / Rrim(I) all: 0.793

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→51 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.882 / SU B: 15.31 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26839 1784 5 %RANDOM
Rwork0.21893 ---
obs0.22145 34230 93.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.134 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20.63 Å2-0.21 Å2
2--0.83 Å20.62 Å2
3----1.41 Å2
Refinement stepCycle: 1 / Resolution: 2.27→51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6816 0 48 122 6986
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0127068
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166641
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.8289606
X-RAY DIFFRACTIONr_angle_other_deg0.4161.74615296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3335870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.908541
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.585101174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0550.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028304
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021613
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_it2.5614.6063475
X-RAY DIFFRACTIONr_mcbond_other2.5614.6063475
X-RAY DIFFRACTIONr_mcangle_it4.2838.284340
X-RAY DIFFRACTIONr_mcangle_other4.2838.2814341
X-RAY DIFFRACTIONr_scbond_it2.5344.8973593
X-RAY DIFFRACTIONr_scbond_other2.5344.8973594
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3128.9215265
X-RAY DIFFRACTIONr_long_range_B_refined8.56246.788257
X-RAY DIFFRACTIONr_long_range_B_other8.56346.88253
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.326 Å
RfactorNum. reflection% reflection
Rfree0.34 155 -
Rwork0.304 2366 -
obs--87.6 %

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