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- PDB-7jkr: GTP-specific succinyl-CoA synthetase complexed with Mg-GMPPNP, ph... -

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Basic information

Entry
Database: PDB / ID: 7jkr
TitleGTP-specific succinyl-CoA synthetase complexed with Mg-GMPPNP, 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 (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 / 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
PHOSPHOAMINOPHOSPHONIC 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: 2.64 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 28, 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 1.2Oct 30, 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)75,4405
Polymers74,8022
Non-polymers6393
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-43 kcal/mol
Surface area28290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.328, 99.328, 134.029
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)
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)
References: UniProt: P53590, succinate-CoA ligase (GDP-forming)

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Non-polymers , 4 types, 10 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.55 Å3/Da / Density % sol: 51.84 %
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: 2.64→86.02 Å / Num. obs: 23016 / % possible obs: 100 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.052 / Net I/σ(I): 9.3
Reflection shellResolution: 2.64→2.69 Å / Rmerge(I) obs: 2.191 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 1140 / CC1/2: 0.298 / Rpim(I) all: 0.938

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Processing

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

2fp4


Resolution: 2.64→86.02 Å / SU ML: 0.51 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 33.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2924 1123 4.89 %
Rwork0.2412 21832 -
obs0.2435 22955 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 244.11 Å2 / Biso mean: 117.901 Å2 / Biso min: 52.57 Å2
Refinement stepCycle: final / Resolution: 2.64→86.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5185 0 64 7 5256
Biso mean--105.02 64.42 -
Num. residues----692
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 (%)
2.64-2.760.39161390.36572670280999
2.76-2.910.37571430.335226632806100
2.91-3.090.32711550.34526842839100
3.09-3.330.34071290.294327282857100
3.33-3.660.3211330.269427062839100
3.66-4.190.29441350.229127512886100
4.19-5.280.25181330.211827702903100
5.28-86.020.26831560.203428603016100
Refinement TLS params.Method: refined / Origin x: -7.493 Å / Origin y: 27.9591 Å / Origin z: 12.7257 Å
111213212223313233
T0.4368 Å2-0.0403 Å20.0288 Å2-0.9392 Å2-0.1759 Å2--0.669 Å2
L2.2385 °2-0.1186 °2-0.2537 °2-1.6933 °2-0.0894 °2--1.4447 °2
S0.1459 Å °-0.651 Å °0.0895 Å °0.0618 Å °-0.2207 Å °0.3579 Å °0.0852 Å °-0.37 Å °0.0597 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 306
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allB1 - 392
4X-RAY DIFFRACTION1allB601
5X-RAY DIFFRACTION1allC1
6X-RAY DIFFRACTION1allD1 - 7

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