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- PDB-7jj0: GTP-specific succinyl-CoA synthetase complexed with Mg-GMPPCP -

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Basic information

Entry
Database: PDB / ID: 7jj0
TitleGTP-specific succinyl-CoA synthetase complexed with Mg-GMPPCP
Components
  • Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
  • Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
KeywordsLIGASE / Complex
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / succinate-CoA ligase (ADP-forming) activity / succinyl-CoA metabolic process / tricarboxylic acid cycle / nucleotide binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase (GDP-forming) activity / succinate-CoA ligase complex (ADP-forming) / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase complex / 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, subdomain 1 / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / 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: 2.25 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 24, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
D: Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9976
Polymers149,4514
Non-polymers5462
Water1,856103
1
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)75,2714
Polymers74,7262
Non-polymers5462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-41 kcal/mol
Surface area27320 Å2
MethodPISA
2
C: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
D: Succinate--CoA ligase [GDP-forming] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)74,7262
Polymers74,7262
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-25 kcal/mol
Surface area28420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.311, 99.311, 133.512
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 182 or resid 184 through 306))
21(chain C and (resid 2 through 182 or resid 184 through 269 or resid 271 through 306))
12(chain B and (resid 1 through 42 or resid 46 through 67 or resid 76 through 393))
22chain D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERLEULEU(chain A and (resid 2 through 182 or resid 184 through 306))AA2 - 1821 - 181
121VALVALLEULEU(chain A and (resid 2 through 182 or resid 184 through 306))AA184 - 306183 - 305
211SERSERLEULEU(chain C and (resid 2 through 182 or resid 184 through 269 or resid 271 through 306))CC2 - 1821 - 181
221VALVALGLYGLY(chain C and (resid 2 through 182 or resid 184 through 269 or resid 271 through 306))CC184 - 269183 - 268
231ALAALALEULEU(chain C and (resid 2 through 182 or resid 184 through 269 or resid 271 through 306))CC271 - 306270 - 305
112METMETGLUGLU(chain B and (resid 1 through 42 or resid 46 through 67 or resid 76 through 393))BB1 - 421 - 42
122LYSLYSVALVAL(chain B and (resid 1 through 42 or resid 46 through 67 or resid 76 through 393))BB46 - 6746 - 67
132VALVALTHRTHR(chain B and (resid 1 through 42 or resid 46 through 67 or resid 76 through 393))BB76 - 39376 - 393
212METMETTHRTHRchain DDD1 - 3931 - 393

NCS ensembles :
ID
1
2

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Components

#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.: 2
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 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: 42635.746 Da / Num. of mol.: 2
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)
#3: Chemical ChemComp-GCP / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
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: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 1.0 M sodium citrate, Tris-HCl pH 7.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→133.51 Å / Num. obs: 69914 / % possible obs: 100 % / Redundancy: 5.1 % / CC1/2: 0.907 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.069 / Net I/σ(I): 7.3
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 2.305 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 3417 / CC1/2: 0.371 / Rpim(I) all: 1.159

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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: 2.25→86.01 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 34.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2651 3528 5.07 %
Rwork0.2347 66109 -
obs0.2363 69637 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.56 Å2 / Biso mean: 74.341 Å2 / Biso min: 26.83 Å2
Refinement stepCycle: final / Resolution: 2.25→86.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10238 0 51 103 10392
Biso mean--108.29 44.51 -
Num. residues----1368
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2682X-RAY DIFFRACTION8.696TORSIONAL
12C2682X-RAY DIFFRACTION8.696TORSIONAL
21B3529X-RAY DIFFRACTION8.696TORSIONAL
22D3529X-RAY DIFFRACTION8.696TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.280.40611240.37112535265995
2.28-2.310.40951230.36772677280099
2.31-2.350.35281460.35542578272499
2.35-2.380.36121080.35482677278599
2.38-2.420.37661620.340526282790100
2.42-2.470.31461260.339726732799100
2.47-2.510.30611220.320526342756100
2.51-2.560.35581740.314626682842100
2.56-2.610.32871540.316826382792100
2.61-2.670.35751560.314526002756100
2.67-2.730.34941740.299526402814100
2.73-2.80.30611380.307226212759100
2.8-2.870.31821280.301226872815100
2.87-2.960.33771160.285326662782100
2.96-3.050.3391990.279226882787100
3.05-3.160.3321400.26226482788100
3.16-3.290.25681520.259826492801100
3.29-3.440.26071500.251326972847100
3.44-3.620.29311850.228125702755100
3.62-3.850.27221230.220926822805100
3.85-4.140.23071460.194426562802100
4.14-4.560.23051360.188326492785100
4.56-5.220.20831520.186226582810100
5.22-6.580.20991390.204926602799100
6.58-86.010.20841550.171226302785100

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