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- PDB-7jmk: GTP-specific succinyl-CoA synthetase complexed with Mg-GDP in spa... -

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Basic information

Entry
Database: PDB / ID: 7jmk
TitleGTP-specific succinyl-CoA synthetase complexed with Mg-GDP in space group P32
Components
  • (Succinate--CoA ligase ...) x 2
  • 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: 2.5 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
DepositionAug 1, 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
Revision 1.2Nov 6, 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

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: Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,9956
Polymers149,5274
Non-polymers4682
Water1,18966
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)75,1934
Polymers74,7262
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-50 kcal/mol
Surface area27750 Å2
MethodPISA
2
C: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
D: Succinyl-CoA ligase [GDP-forming] subunit beta, mitochondrial


Theoretical massNumber of molelcules
Total (without water)74,8022
Polymers74,8022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-25 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.762, 99.762, 134.206
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 253 or resid 258 or resid 260 through 306))
21(chain C and (resid 2 through 182 or resid 184 through 264 or resid 270 through 306))
12(chain B and (resid 1 through 24 or resid 38...
22(chain D and (resid 1 through 58 or resid 64 through 331 or resid 333 through 393))

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 253 or resid 258 or resid 260 through 306))AA2 - 1821 - 181
121VALVALPROPRO(chain A and (resid 2 through 182 or resid 184 through 253 or resid 258 or resid 260 through 306))AA184 - 253183 - 252
131GLYGLYGLYGLY(chain A and (resid 2 through 182 or resid 184 through 253 or resid 258 or resid 260 through 306))AA258257
141ALAALALEULEU(chain A and (resid 2 through 182 or resid 184 through 253 or resid 258 or resid 260 through 306))AA260 - 306259 - 305
211SERSERLEULEU(chain C and (resid 2 through 182 or resid 184 through 264 or resid 270 through 306))CC2 - 1821 - 181
221VALVALILEILE(chain C and (resid 2 through 182 or resid 184 through 264 or resid 270 through 306))CC184 - 264183 - 263
231GLYGLYLEULEU(chain C and (resid 2 through 182 or resid 184 through 264 or resid 270 through 306))CC270 - 306269 - 305
112METMETVALVAL(chain B and (resid 1 through 24 or resid 38...BB1 - 241 - 24
122LEULEUGLUGLU(chain B and (resid 1 through 24 or resid 38...BB38 - 4238 - 42
132LYSLYSGLYGLY(chain B and (resid 1 through 24 or resid 38...BB46 - 5246 - 52
142LYSLYSGLYGLY(chain B and (resid 1 through 24 or resid 38...BB64 - 6564 - 65
152VALVALVALVAL(chain B and (resid 1 through 24 or resid 38...BB7575
162LYSLYSLYSLYS(chain B and (resid 1 through 24 or resid 38...BB8181
172GLYGLYASNASN(chain B and (resid 1 through 24 or resid 38...BB85 - 33185 - 331
182ALAALATHRTHR(chain B and (resid 1 through 24 or resid 38...BB333 - 393333 - 393
212METMETVALVAL(chain D and (resid 1 through 58 or resid 64 through 331 or resid 333 through 393))DD1 - 581 - 58
222LYSLYSASNASN(chain D and (resid 1 through 58 or resid 64 through 331 or resid 333 through 393))DD64 - 33164 - 331
232ALAALATHRTHR(chain D and (resid 1 through 58 or resid 64 through 331 or resid 333 through 393))DD333 - 393333 - 393

NCS ensembles :
ID
1
2

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Components

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Succinate--CoA ligase ... , 2 types, 3 molecules ACB

#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.: 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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Protein , 1 types, 1 molecules D

#3: 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 , 3 types, 68 molecules

#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 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.58 Å3/Da / Density % sol: 52.27 %
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: 2.5→72.65 Å / Num. obs: 51719 / % possible obs: 100 % / Redundancy: 4.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.045 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 2593 / CC1/2: 0.84 / Rpim(I) all: 0.259

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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: 2.5→53 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2694 2676 5.19 %
Rwork0.2399 48918 -
obs0.2415 51594 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 276.97 Å2 / Biso mean: 99.9117 Å2 / Biso min: 37.43 Å2
Refinement stepCycle: final / Resolution: 2.5→53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9955 0 87 66 10108
Biso mean--115.66 51.32 -
Num. residues----1327
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2701X-RAY DIFFRACTION9.166TORSIONAL
12C2701X-RAY DIFFRACTION9.166TORSIONAL
21B3190X-RAY DIFFRACTION9.166TORSIONAL
22D3190X-RAY DIFFRACTION9.166TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.550.35691560.36472523267998
2.55-2.590.37511510.354125472698100
2.59-2.650.37051520.342926052757100
2.65-2.70.34951660.336725552721100
2.71-2.770.34711320.33925732705100
2.77-2.840.30971660.328625402706100
2.84-2.910.3256800.321426092689100
2.91-30.33291320.308725952727100
3-3.10.3209950.296726472742100
3.1-3.210.32421320.279625832715100
3.21-3.340.2861680.273625702738100
3.34-3.490.31591500.267925482698100
3.49-3.670.28711630.237425512714100
3.67-3.90.28531250.231926062731100
3.9-4.20.22421420.212225702712100
4.2-4.620.22481400.205425942734100
4.62-5.290.23591420.196125772719100
5.29-6.660.24661370.229625812718100
6.67-530.22821470.18162544269199
Refinement TLS params.Method: refined / Origin x: -9.1914 Å / Origin y: 18.052 Å / Origin z: 32.2748 Å
111213212223313233
T0.4247 Å20.0241 Å20.0539 Å2-0.3546 Å2-0.0298 Å2--0.4038 Å2
L2.203 °20.8719 °2-0.1306 °2-1.4944 °2-0.1219 °2--1.0089 °2
S0.1049 Å °0.332 Å °-0.0489 Å °0.2205 Å °-0.1318 Å °0.0214 Å °0.26 Å °0.0151 Å °0.047 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 306
2X-RAY DIFFRACTION1allB1 - 401
3X-RAY DIFFRACTION1allC2 - 306
4X-RAY DIFFRACTION1allD1 - 393
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1 - 66

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