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- PDB-7jfp: GTP-specific succinyl-CoA synthetase complexed with Mg-GDP, phosp... -

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Basic information

Entry
Database: PDB / ID: 7jfp
TitleGTP-specific succinyl-CoA synthetase complexed with Mg-GDP, phosphohistidine loop pointing towards nucleotide binding site
Components
  • Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
  • Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial
KeywordsLIGASE / Complex
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 / 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 ...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 / 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
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / 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 / Resolution: 2.55 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.D / Year: 2021
Title: Second distinct conformation of the phosphohistidine loop in succinyl-CoA synthetase
Authors: Huang, J. / Fraser, M.E.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinate--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)75,5467
Polymers74,8022
Non-polymers7445
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-46 kcal/mol
Surface area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.645, 99.645, 134.262
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

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


Mass: 32089.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG1 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: SUCLG2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P53590, succinate-CoA ligase (GDP-forming)

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Non-polymers , 4 types, 11 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 1.0 M sodium citrate, Tris-HCl pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→52.99 Å / Num. obs: 25660 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.063 / Net I/σ(I): 8.1
Reflection shellResolution: 2.55→2.59 Å / Mean I/σ(I) obs: 0.2 / Num. unique obs: 1278 / CC1/2: 0.297

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIXdev_3885refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FP4

2fp4


Resolution: 2.55→52.99 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 34.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.293 1131 4.88 %
Rwork0.2399 22066 -
obs0.2423 23197 90.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 283.58 Å2 / Biso mean: 113.4011 Å2 / Biso min: 48.63 Å2
Refinement stepCycle: final / Resolution: 2.55→52.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5212 0 125 6 5343
Biso mean--117.01 56.46 -
Num. residues----696
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.670.3883500.4081092114236
2.67-2.810.38831450.36792660280588
2.81-2.980.3641610.35992941310298
2.98-3.210.33951670.304230293196100
3.21-3.540.32571370.293730283165100
3.54-4.050.2861630.233830283191100
4.05-5.10.25631340.2143098323299
5.1-52.990.27581740.19773190336499
Refinement TLS params.Method: refined / Origin x: -7.3836 Å / Origin y: 28.0442 Å / Origin z: 13.0689 Å
111213212223313233
T0.3432 Å2-0.0501 Å20.056 Å2-0.7473 Å2-0.1469 Å2--0.6988 Å2
L2.2967 °2-0.1746 °2-0.0753 °2-1.4443 °2-0.0025 °2--1.2388 °2
S0.0687 Å °-0.5674 Å °0.0836 Å °0.0873 Å °-0.1731 Å °0.3487 Å °0.0824 Å °-0.3154 Å °0.0823 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 306
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allB1 - 393
4X-RAY DIFFRACTION1allB401 - 601
5X-RAY DIFFRACTION1allC1 - 6
6X-RAY DIFFRACTION1allD1

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