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- PDB-4xx0: CoA bound to pig GTP-specific succinyl-CoA synthetase -

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Basic information

Entry
Database: PDB / ID: 4xx0
TitleCoA bound to pig GTP-specific succinyl-CoA synthetase
Components(Succinyl-CoA ligase ...) x 2
KeywordsLIGASE / ATP-grasp fold
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding / GTP binding / mitochondrion / ATP binding / metal ion binding
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, A domain / ATP-grasp fold, B domain / ATP-grasp fold, subdomain 1 / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / PHOSPHATE ION / Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial / Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsFraser, M.E. / Huang, J. / Malhi, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of GTP-specific succinyl-CoA synthetase in complex with CoA.
Authors: Huang, J. / Malhi, M. / Deneke, J. / Fraser, M.E.
History
DepositionJan 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)77,55813
Polymers75,8432
Non-polymers1,71511
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-113 kcal/mol
Surface area27510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.340, 82.500, 49.380
Angle α, β, γ (deg.)90.000, 104.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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

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


Mass: 33131.016 Da / Num. of mol.: 1 / Fragment: UNP residues 42-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG1 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O19069, succinate-CoA ligase (GDP-forming), succinate-CoA ligase (ADP-forming)
#2: Protein Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial / GTP-specific succinyl-CoA synthetase subunit beta / Succinyl-CoA synthetase beta-G chain / SCS-betaG


Mass: 42711.867 Da / Num. of mol.: 1 / Fragment: UNP residues 40-433
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG2 / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P53590, succinate-CoA ligase (GDP-forming)

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Non-polymers , 5 types, 204 molecules

#3: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, 2-Mercaptoethanol, Na/K phosphate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 6, 2013
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97795 Å / Relative weight: 1
ReflectionResolution: 2.1→41.399 Å / Num. all: 36903 / Num. obs: 36903 / % possible obs: 94.6 % / Redundancy: 3.1 % / Biso Wilson estimate: 25.37 Å2 / Rpim(I) all: 0.075 / Rrim(I) all: 0.138 / Rsym value: 0.115 / Net I/av σ(I): 3.836 / Net I/σ(I): 5.9 / Num. measured all: 114697
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.2130.4541.41561951920.3090.4542.691.6
2.21-2.353.10.31111550650410.2190.3113.293.8
2.35-2.513.10.18741496248140.1230.1873.995.5
2.51-2.713.10.1691.91404145040.1150.1694.895.1
2.71-2.973.10.1195.81301441630.0760.1195.995.8
2.97-3.323.10.0996.61182437910.0630.0997.395.8
3.32-3.833.10.0994.91036933270.0630.0999.295.9
3.83-4.73.20.0856.7880027830.0540.08510.695.7
4.7-6.643.20.0857.2686621510.0530.08510.394.8
6.64-41.3993.30.0728369611370.0450.0721192.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
SCALA3.3.21data scaling
iMOSFLMdata reduction
PDB_EXTRACT3.15data extraction
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→41.399 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 3584 9.73 %
Rwork0.185 33256 -
obs0.1894 36840 93.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.1 Å2 / Biso mean: 31.8187 Å2 / Biso min: 9.84 Å2
Refinement stepCycle: final / Resolution: 2.1→41.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 101 193 5502
Biso mean--34.6 31.33 -
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025384
X-RAY DIFFRACTIONf_angle_d0.6117280
X-RAY DIFFRACTIONf_chiral_restr0.024828
X-RAY DIFFRACTIONf_plane_restr0.003959
X-RAY DIFFRACTIONf_dihedral_angle_d12.1552016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.12770.27461070.22171228133590
2.1277-2.15680.31461200.25911240136090
2.1568-2.18760.40531140.32531268138292
2.1876-2.22030.24461150.24551260137592
2.2203-2.2550.33351150.27131277139291
2.255-2.29190.26511350.24111257139294
2.2919-2.33140.28511500.20471273142393
2.3314-2.37380.25521280.20561271139995
2.3738-2.41950.26761410.19311292143395
2.4195-2.46890.25311490.1981275142493
2.4689-2.52250.28741540.19351292144697
2.5225-2.58120.24461480.19161258140693
2.5812-2.64570.24431370.19881291142896
2.6457-2.71730.23571470.19911287143494
2.7173-2.79720.29121310.19111308143996
2.7972-2.88750.24511500.18881270142095
2.8875-2.99060.26541350.19531344147997
2.9906-3.11040.25721590.19581269142895
3.1104-3.25190.22091550.18691294144996
3.2519-3.42320.21281590.17391298145796
3.4232-3.63760.21071390.16851285142495
3.6376-3.91820.19891240.16261334145895
3.9182-4.31220.19051600.15491265142595
4.3122-4.93530.19831400.14611288142893
4.9353-6.21460.19721440.17221272141693
6.2146-41.40660.1561280.15011260138889

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