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

ID or keywords:

Entry

Database: PDB / ID: 3oxo

Title

Succinyl-CoA:3-ketoacid CoA transferase from pig heart covalently bound to CoA

Components

Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

Keywords

TRANSFERASE / 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

Biological species

Sus scrofa (pig)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Fraser, M.E.

Citation

Journal: 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

Deposition	Sep 21, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 10, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: 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 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3oxo.cif.gz	696.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3oxo.ent.gz	578.3 KB	Display	PDB format
PDBx/mmJSON format	3oxo.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3oxo_validation.pdf.gz	1.3 MB	Display	wwPDB validaton report
Full document	3oxo_full_validation.pdf.gz	1.4 MB	Display
Data in XML	3oxo_validation.xml.gz	124.1 KB	Display
Data in CIF	3oxo_validation.cif.gz	169.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ox/3oxo ftp://data.pdbj.org/pub/pdb/validation_reports/ox/3oxo	HTTPS FTP

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Related structure data

Related structure data	2nrbS 1m3e 1ooy 1ooz 1ope 2nrc S: Starting model for refinement
Similar structure data	3k6m-1 2nrc-2 2nrc-1 3dlx-1 3k6m-2 3cdk-d 1ooy-d 1ope-d 1m3e-2 3dlx-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#146 - Feb 2012 Aminoglycoside Antibiotics similarity (1) #93 - Sep 2007 Citrate Synthase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1) #39 - Mar 2003 lac Repressor similarity (1)

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

430 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

B: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

hetero molecules

defined by author&software
107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

hetero molecules

defined by author&software
107 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

F: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

hetero molecules

defined by author&software
108 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

H: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial

hetero molecules

defined by author&software
108 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3
4
5

#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 modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.22 Å³/Da / Density % sol: 44.66 %
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 200 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
Detector	Type: 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
Radiation	Monochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.11588 Å / Relative weight: 1
Reflection	Resolution: 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 % / B_iso Wilson estimate: 39 Å² / R_merge(I) obs: 0.086 / Net I/σ(I): 5.9
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 1.8 % / R_merge(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

Name	Version	Classification
ADSC	Quantum	data collection
AMoRE		phasing
REFMAC	5.5.0102	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2NRB

2nrb

Resolution: 2.3→21.2 Å / Cor.coef. F_o:F_c: 0.914 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27339	7517	5 %	RANDOM
R_work	0.24523	-	-	-
all	0.24665	149072	-	-
obs	0.24665	149072	91.44 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.249 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.1 Å²	-1.27 Å²	1.12 Å²
2-	-	5.73 Å²	1.39 Å²
3-	-	-	-3.38 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→21.2 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	28269	0	195	440	28904

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.022	28937
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	19697
X-RAY DIFFRACTION	r_angle_refined_deg	0.933	1.983	39088
X-RAY DIFFRACTION	r_angle_other_deg	0.759	3	48330
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.407	5	3694
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.784	24.841	1167
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.886	15	5180
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.12	15	145
X-RAY DIFFRACTION	r_chiral_restr	0.055	0.2	4446
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	31947
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	5426
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.15	1.5	18301
X-RAY DIFFRACTION	r_mcbond_other	0.301	1.5	7645
X-RAY DIFFRACTION	r_mcangle_it	1.983	2	29374
X-RAY DIFFRACTION	r_scbond_it	3.11	3	10636
X-RAY DIFFRACTION	r_scangle_it	4.88	4.5	9714
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	3020	LOOSE POSITIONAL	0.02	0.05
1	2	B	3020	LOOSE POSITIONAL	0.02	0.05
1	3	C	3020	LOOSE POSITIONAL	0.02	0.05
1	4	D	3020	LOOSE POSITIONAL	0.02	0.05
1	5	E	3020	LOOSE POSITIONAL	0.01	0.05
1	6	F	3020	LOOSE POSITIONAL	0.02	0.05
1	7	G	3020	LOOSE POSITIONAL	0.02	0.05
1	8	H	3020	LOOSE POSITIONAL	0.01	0.05
1	1	A	3020	LOOSE THERMAL	7.64	20
1	2	B	3020	LOOSE THERMAL	4.26	20
1	3	C	3020	LOOSE THERMAL	3.64	20
1	4	D	3020	LOOSE THERMAL	4.29	20
1	5	E	3020	LOOSE THERMAL	3.4	20
1	6	F	3020	LOOSE THERMAL	4.45	20
1	7	G	3020	LOOSE THERMAL	5.17	20
1	8	H	3020	LOOSE THERMAL	10.94	20
2	1	A	2787	LOOSE POSITIONAL	0.02	0.05
2	2	B	2787	LOOSE POSITIONAL	0.01	0.05
2	3	C	2787	LOOSE POSITIONAL	0.02	0.05
2	4	D	2787	LOOSE POSITIONAL	0.01	0.05
2	1	A	2787	LOOSE THERMAL	5.88	20
2	2	B	2787	LOOSE THERMAL	2.48	20
2	3	C	2787	LOOSE THERMAL	3.18	20
2	4	D	2787	LOOSE THERMAL	6.08	20
3	1	E	2621	LOOSE POSITIONAL	0.01	0.05
3	2	F	2621	LOOSE POSITIONAL	0.01	0.05
3	3	G	2621	LOOSE POSITIONAL	0.01	0.05
3	4	H	2621	LOOSE POSITIONAL	0.01	0.05
3	1	E	2621	LOOSE THERMAL	4.44	20
3	2	F	2621	LOOSE THERMAL	5.37	20
3	3	G	2621	LOOSE THERMAL	3.71	20
3	4	H	2621	LOOSE THERMAL	8.44	20
4	1	E	59	LOOSE POSITIONAL	0.01	0.05
4	2	G	59	LOOSE POSITIONAL	0.01	0.05
4	3	H	59	LOOSE POSITIONAL	0.01	0.05
4	1	E	59	LOOSE THERMAL	1.41	20
4	2	G	59	LOOSE THERMAL	2.47	20
4	3	H	59	LOOSE THERMAL	3.28	20
5	1	E	70	LOOSE POSITIONAL	0.01	0.05
5	2	F	70	LOOSE POSITIONAL	0.01	0.05
5	3	G	70	LOOSE POSITIONAL	0.01	0.05
5	4	H	70	LOOSE POSITIONAL	0.01	0.05
5	1	E	70	LOOSE THERMAL	4.51	20
5	2	F	70	LOOSE THERMAL	3.38	20
5	3	G	70	LOOSE THERMAL	8.1	20
5	4	H	70	LOOSE THERMAL	13.18	20

LS refinement shell

Resolution: 2.3→2.359 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.408	478	-
R_work	0.352	8825	-
obs	-	9303	79.34 %

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