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- PDB-3oxo: Succinyl-CoA:3-ketoacid CoA transferase from pig heart covalently... -

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Basic information

Entry
Database: PDB / ID: 3oxo
TitleSuccinyl-CoA:3-ketoacid CoA transferase from pig heart covalently bound to CoA
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
KeywordsTRANSFERASE / ALPHA/BETA PROTEIN
Function / homology
Function and homology information


Utilization of Ketone Bodies / 3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone body metabolic process / ketone body catabolic process / Mitochondrial protein degradation / protein homodimerization activity / mitochondrion
Similarity search - Function
3-oxoacid CoA-transferase / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / 3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / 3-oxoacid CoA-transferase, subunit B / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I ...3-oxoacid CoA-transferase / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / 3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / 3-oxoacid CoA-transferase, subunit B / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsFraser, M.E.
CitationJournal: Biochemistry / Year: 2010
Title: Catalytic role of the conformational change in succinyl-CoA:3-oxoacid CoA transferase on binding CoA.
Authors: Fraser, M.E. / Hayakawa, K. / Brown, W.D.
History
DepositionSep 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
E: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
F: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
G: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
H: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)429,89715
Polymers426,7208
Non-polymers3,1767
Water7,927440
1
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7163
Polymers106,6802
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-28 kcal/mol
Surface area34780 Å2
MethodPISA
2
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,7514
Polymers106,6802
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-39 kcal/mol
Surface area34430 Å2
MethodPISA
3
E: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
F: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2154
Polymers106,6802
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6960 Å2
ΔGint-10 kcal/mol
Surface area32680 Å2
MethodPISA
4
G: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
H: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,2154
Polymers106,6802
Non-polymers1,5352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint-10 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.121, 107.133, 134.565
Angle α, β, γ (deg.)89.60, 80.21, 75.13
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
13E
23F
33G
43H
14E
24G
34H
15E
25F
35G
45H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A1 - 56
2116B1 - 56
3116C1 - 56
4116D1 - 56
5116E1 - 56
6116F1 - 56
7116G1 - 56
8116H1 - 56
1216A58 - 82
2216B58 - 82
3216C58 - 82
4216D58 - 82
5216E58 - 82
6216F58 - 82
7216G58 - 82
8216H58 - 82
1316A84 - 127
2316B84 - 127
3316C84 - 127
4316D84 - 127
5316E84 - 127
6316F84 - 127
7316G84 - 127
8316H84 - 127
1416A129 - 136
2416B129 - 136
3416C129 - 136
4416D129 - 136
5416E129 - 136
6416F129 - 136
7416G129 - 136
8416H129 - 136
1516A142 - 177
2516B142 - 177
3516C142 - 177
4516D142 - 177
5516E142 - 177
6516F142 - 177
7516G142 - 177
8516H142 - 177
1616A179 - 210
2616B179 - 210
3616C179 - 210
4616D179 - 210
5616E179 - 210
6616F179 - 210
7616G179 - 210
8616H179 - 210
1716A212 - 242
2716B212 - 242
3716C212 - 242
4716D212 - 242
5716E212 - 242
6716F212 - 242
7716G212 - 242
8716H212 - 242
1126A262 - 317
2126B262 - 317
3126C262 - 317
4126D262 - 317
1226A319 - 480
2226B319 - 480
3226C319 - 480
4226D319 - 480
1136E267 - 450
2136F267 - 450
3136G267 - 450
4136H267 - 450
1236E455 - 480
2236F455 - 480
3236G455 - 480
4236H455 - 480
1146E451 - 454
2146G451 - 454
3146H451 - 454
1156E1305
2156F1305
3156G1305
4156H1305

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial / 3-oxoacid-CoA transferase 1 / Somatic-type succinyl-CoA:3-oxoacid CoA-transferase / SCOT-s


Mass: 53340.055 Da / Num. of mol.: 8 / Fragment: unp residues 40-517
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: OXCT, OXCT1, SCOT / Plasmid: pET-42b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q29551, 3-oxoacid CoA-transferase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / Source method: isolated from a natural source / Formula: H2O
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: 2.22 Å3/Da / Density % sol: 44.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG3350, 100 mM TrisHCl, potassium citrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 30, 2007
Details: Crystal type Si(111), Mirrors M1: plane parabola Pt and Rh-coated Invar steel M2: torroid (2:1 demagnification) Pt and Rh-coated Si
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 2.3→21.2 Å / Num. all: 149078 / Num. obs: 149078 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 5.9
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 2.3 / Num. unique all: 19645 / % possible all: 82.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2NRB

2nrb


Resolution: 2.3→21.2 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.896 / SU B: 10.804 / SU ML: 0.253 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.298 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27339 7517 5 %RANDOM
Rwork0.24523 ---
all0.24665 149072 --
obs0.24665 149072 91.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.249 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å2-1.27 Å21.12 Å2
2--5.73 Å21.39 Å2
3----3.38 Å2
Refinement stepCycle: LAST / Resolution: 2.3→21.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28269 0 195 440 28904
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02228937
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219697
X-RAY DIFFRACTIONr_angle_refined_deg0.9331.98339088
X-RAY DIFFRACTIONr_angle_other_deg0.759348330
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.40753694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78424.8411167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.886155180
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1215145
X-RAY DIFFRACTIONr_chiral_restr0.0550.24446
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02131947
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025426
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.151.518301
X-RAY DIFFRACTIONr_mcbond_other0.3011.57645
X-RAY DIFFRACTIONr_mcangle_it1.983229374
X-RAY DIFFRACTIONr_scbond_it3.11310636
X-RAY DIFFRACTIONr_scangle_it4.884.59714
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3020LOOSE POSITIONAL0.020.05
12B3020LOOSE POSITIONAL0.020.05
13C3020LOOSE POSITIONAL0.020.05
14D3020LOOSE POSITIONAL0.020.05
15E3020LOOSE POSITIONAL0.010.05
16F3020LOOSE POSITIONAL0.020.05
17G3020LOOSE POSITIONAL0.020.05
18H3020LOOSE POSITIONAL0.010.05
11A3020LOOSE THERMAL7.6420
12B3020LOOSE THERMAL4.2620
13C3020LOOSE THERMAL3.6420
14D3020LOOSE THERMAL4.2920
15E3020LOOSE THERMAL3.420
16F3020LOOSE THERMAL4.4520
17G3020LOOSE THERMAL5.1720
18H3020LOOSE THERMAL10.9420
21A2787LOOSE POSITIONAL0.020.05
22B2787LOOSE POSITIONAL0.010.05
23C2787LOOSE POSITIONAL0.020.05
24D2787LOOSE POSITIONAL0.010.05
21A2787LOOSE THERMAL5.8820
22B2787LOOSE THERMAL2.4820
23C2787LOOSE THERMAL3.1820
24D2787LOOSE THERMAL6.0820
31E2621LOOSE POSITIONAL0.010.05
32F2621LOOSE POSITIONAL0.010.05
33G2621LOOSE POSITIONAL0.010.05
34H2621LOOSE POSITIONAL0.010.05
31E2621LOOSE THERMAL4.4420
32F2621LOOSE THERMAL5.3720
33G2621LOOSE THERMAL3.7120
34H2621LOOSE THERMAL8.4420
41E59LOOSE POSITIONAL0.010.05
42G59LOOSE POSITIONAL0.010.05
43H59LOOSE POSITIONAL0.010.05
41E59LOOSE THERMAL1.4120
42G59LOOSE THERMAL2.4720
43H59LOOSE THERMAL3.2820
51E70LOOSE POSITIONAL0.010.05
52F70LOOSE POSITIONAL0.010.05
53G70LOOSE POSITIONAL0.010.05
54H70LOOSE POSITIONAL0.010.05
51E70LOOSE THERMAL4.5120
52F70LOOSE THERMAL3.3820
53G70LOOSE THERMAL8.120
54H70LOOSE THERMAL13.1820
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 478 -
Rwork0.352 8825 -
obs-9303 79.34 %

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