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- PDB-5cae: Succinate bound to pig GTP-specific succinyl-CoA synthetase -

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Basic information

Entry
Database: PDB / ID: 5cae
TitleSuccinate bound to pig GTP-specific succinyl-CoA synthetase
Components(Succinyl-CoA ligase ...) x 2
KeywordsLIGASE
Function / homology
Function and homology information


succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / tricarboxylic acid cycle / nucleotide binding ...succinate-CoA ligase (GDP-forming) / succinate-CoA ligase complex / succinate-CoA ligase complex (ADP-forming) / succinate-CoA ligase (GDP-forming) activity / succinyl-CoA metabolic process / Citric acid cycle (TCA cycle) / succinate-CoA ligase (ADP-forming) / succinate-CoA ligase (ADP-forming) activity / 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 / SUCCINIC ACID / 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: 2.2 Å
AuthorsHuang, J. / Fraser, M.E.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Structural basis for the binding of succinate to succinyl-CoA synthetase.
Authors: Huang, J. / Fraser, M.E.
History
DepositionJun 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Aug 17, 2016Group: Database references
Revision 1.3Sep 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 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)77,0239
Polymers75,7992
Non-polymers1,2257
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7130 Å2
ΔGint-46 kcal/mol
Surface area26920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.670, 81.020, 50.780
Angle α, β, γ (deg.)90.000, 104.900, 90.000
Int Tables number4
Space group name H-MP1211
DetailsSDS-PAGE/Gel filtration (G100 Sephadex) confirms the heterodimer.

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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: 42667.809 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 , 7 types, 257 molecules

#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-SIN / SUCCINIC ACID / Succinic acid


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, ammonium succinate, magnesium chloride, CoA, HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97947 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Sep 20, 2014
RadiationMonochromator: KOHZU double crystal monochromator (DCM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2.2→49.073 Å / Num. all: 33544 / Num. obs: 33544 / % possible obs: 97 % / Redundancy: 3.6 % / Biso Wilson estimate: 26.81 Å2 / Rpim(I) all: 0.058 / Rrim(I) all: 0.113 / Rsym value: 0.096 / Net I/av σ(I): 6.964 / Net I/σ(I): 9.3 / Num. measured all: 122021
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.323.50.4661.61660547500.2840.4662.694.6
2.32-2.463.60.3462.21650346060.210.3463.496.5
2.46-2.633.70.2652.91581243140.1590.2654.597.2
2.63-2.843.70.1923.91503540730.1160.1926.397.4
2.84-3.113.70.135.81383037370.0780.138.797.2
3.11-3.483.70.0838.51255134000.050.08312.697.9
3.48-4.023.70.0669.71109030060.040.06617.397.7
4.02-4.923.70.04713.7935325410.0280.04720.997.9
4.92-6.963.70.04713728119940.0290.04718.497.8
6.96-49.0733.50.02821.8396111230.0170.02820.797.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.21data scaling
iMOSFLMdata reduction
Cootmodel building
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4XX0

4xx0


Resolution: 2.2→49.073 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 3327 9.92 %
Rwork0.1646 30208 -
obs0.1695 33535 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.03 Å2 / Biso mean: 30.7228 Å2 / Biso min: 13.89 Å2
Refinement stepCycle: final / Resolution: 2.2→49.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5205 0 75 250 5530
Biso mean--26.54 33.66 -
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035358
X-RAY DIFFRACTIONf_angle_d0.5427241
X-RAY DIFFRACTIONf_chiral_restr0.044827
X-RAY DIFFRACTIONf_plane_restr0.003961
X-RAY DIFFRACTIONf_dihedral_angle_d10.8133254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.23140.24661130.21321211132493
2.2314-2.26470.31461320.22521254138695
2.2647-2.30010.25641290.21351212134195
2.3001-2.33780.26291340.19741257139196
2.3378-2.37810.27371410.20251204134596
2.3781-2.42140.23111410.19181290143197
2.4214-2.4680.24411380.18041226136497
2.468-2.51830.25071480.1871258140697
2.5183-2.57310.26211340.17691233136797
2.5731-2.63290.23881520.17221236138897
2.6329-2.69880.24911440.16391282142697
2.6988-2.77170.2221280.16751269139798
2.7717-2.85330.22251440.16471236138098
2.8533-2.94540.19431310.16141275140698
2.9454-3.05060.20151430.15611250139397
3.0506-3.17280.23431450.16461293143898
3.1728-3.31710.19741490.15321232138198
3.3171-3.4920.18391510.14681259141098
3.492-3.71070.20831310.15171293142498
3.7107-3.99710.19051230.15131278140198
3.9971-4.39910.18461600.1381255141598
4.3991-5.03510.18561380.14941294143298
5.0351-6.34150.19881470.18521289143698
6.3415-49.08480.20841310.15641322145398

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