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- PDB-7mss: Human E105Qa GTP-specific succinyl-CoA synthetase complexed with ... -

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Basic information

Entry
Database: PDB / ID: 7mss
TitleHuman E105Qa GTP-specific succinyl-CoA synthetase complexed with succinate, magnesium ion and CoA
Components(Succinate--CoA ligase ...) x 2
KeywordsLIGASE / Complex
Function / homology
Function and homology information


succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinate metabolic process / succinyl-CoA catabolic process / succinyl-CoA metabolic process ...succinate-CoA ligase complex (GDP-forming) / succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinate metabolic process / succinyl-CoA catabolic process / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / tricarboxylic acid cycle / Mitochondrial protein degradation / GDP binding / mitochondrial matrix / nucleotide binding / protein-containing complex binding / GTP binding / magnesium ion binding / mitochondrion / RNA binding / ATP binding / plasma membrane
Similarity search - Function
Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. ...Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / Succinyl-CoA ligase, alpha subunit / Succinate--CoA synthetase, beta subunit / ATP-grasp fold, succinyl-CoA synthetase-type / ATP-grasp domain / Succinyl-CoA synthetase domains / ATP-citrate lyase/succinyl-CoA ligase, active site / ATP-citrate lyase/succinyl-CoA ligase, conserved site / ATP-citrate lyase / succinyl-CoA ligases family active site. / ATP-citrate lyase / succinyl-CoA ligases family signature 1. / Succinyl-CoA synthetase, beta subunit, conserved site / ATP-citrate lyase / succinyl-CoA ligases family signature 3. / ATP-citrate lyase/succinyl-CoA ligase / CoA-ligase / CoA binding domain / Succinyl-CoA synthetase-like / CoA binding domain / CoA-binding / ATP-grasp fold, subdomain 1 / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / PHOSPHATE ION / SUCCINIC ACID / Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHuang, J. / Fraser, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)04815-2019 Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: The structure of succinyl-CoA synthetase bound to the succinyl-phosphate intermediate clarifies the catalytic mechanism of ATP-citrate lyase
Authors: Huang, J. / Fraser, M.E.
History
DepositionMay 12, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
B: Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,52710
Polymers76,1542
Non-polymers1,3738
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-39 kcal/mol
Surface area27020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.471, 81.092, 54.486
Angle α, β, γ (deg.)90.000, 103.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Succinate--CoA ligase ... , 2 types, 2 molecules AB

#1: Protein Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinyl-CoA synthetase subunit alpha / SCS-alpha


Mass: 33526.363 Da / Num. of mol.: 1 / Mutation: E105Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53597, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming)
#2: Protein Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial / GTP-specific succinyl-CoA synthetase subunit beta / GTPSCS / Succinyl-CoA synthetase beta-G chain / SCS-betaG


Mass: 42627.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SUCLG2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q96I99, succinate-CoA ligase (GDP-forming)

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Non-polymers , 6 types, 281 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 22.5% (w/v) PEG3350, 100 mM Ammonium succinate pH 7.5, 100 mM Tris-HCl 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Feb 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→56.32 Å / Num. obs: 66677 / % possible obs: 97.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 30.28 Å2 / Rpim(I) all: 0.051 / Rrim(I) all: 0.093 / Net I/σ(I): 12.4 / Num. measured all: 215571
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.75-1.783.30.51083832521.1572.13195.2
4.75-56.353.463.61190935030.0180.03399.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia23.4.2data scaling
PDB_EXTRACT3.27data extraction
Cootmodel building
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CAE

5cae


Resolution: 1.75→53.01 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2269 4846 7.29 %
Rwork0.2019 61584 -
obs0.2041 66430 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.84 Å2 / Biso mean: 42.4354 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: final / Resolution: 1.75→53.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5244 0 155 273 5672
Biso mean--37.2 38.93 -
Num. residues----700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.4604810.41581989207092
1.77-1.790.4024980.3872064216294
1.79-1.810.3761190.36892027214694
1.81-1.840.3669780.36112075215396
1.84-1.860.36451130.35182065217897
1.86-1.890.2586850.32742116220195
1.89-1.910.3539950.30462100219597
1.91-1.940.3371070.29732057216495
1.94-1.970.35531110.27432078218996
1.97-20.31161020.26562088219096
2-2.040.26181180.25342067218596
2.04-2.080.30581020.24332086218897
2.08-2.120.29651040.26932098220296
2.12-2.160.25481370.23592077221497
2.16-2.210.27711390.22912050218997
2.21-2.260.25821750.22382068224397
2.26-2.310.23951990.2332022222197
2.31-2.380.29142020.22852029223197
2.38-2.450.25652210.20921983220498
2.45-2.520.26972310.20661991222298
2.52-2.610.27472090.20062047225698
2.61-2.720.23872420.19582002224498
2.72-2.840.24022170.20411993221098
2.84-2.990.24942110.20862052226398
2.99-3.180.24992300.20192017224798
3.18-3.430.19992230.19212048227199
3.43-3.770.21872280.17062040226899
3.77-4.320.16712170.14732062227999
4.32-5.440.17522390.14122080231999
5.44-53.010.20132130.17122113232699

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