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- PDB-3k6m: Dynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase... -

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Basic information

Entry
Database: PDB / ID: 3k6m
TitleDynamic domains of Succinyl-CoA:3-ketoacid-coenzyme A transferase from pig heart.
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
KeywordsTRANSFERASE / SCOT / CoA Transferase / dynamic domain / glycerol / Mitochondrion / Transit peptide
Function / homology
Function and homology information


Utilization of Ketone Bodies / cellular ketone body metabolic process / 3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone body catabolic process / Mitochondrial protein degradation / protein homodimerization activity / mitochondrion
Similarity search - Function
3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / 3-oxoacid CoA-transferase, subunit B / 3-oxoacid CoA-transferase / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / Glutaconate Coenzyme A-transferase / Glutaconate Coenzyme A-transferase / Coenzyme A transferase family I ...3-oxoacid CoA-transferase, subunit A / Coenzyme A transferase active site / 3-oxoacid CoA-transferase, subunit B / 3-oxoacid CoA-transferase / Coenzyme A transferases signature 2. / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / 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
Succinyl-CoA:3-ketoacid coenzyme A transferase 1, mitochondrial
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsCoker, S. / Lloyd, A. / Mitchell, E. / Lewis, G.R. / Shoolingin-Jordan, P. / Coker, A.R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: The high-resolution structure of pig heart succinyl-CoA:3-oxoacid coenzyme A transferase.
Authors: Coker, S.F. / Lloyd, A.J. / Mitchell, E. / Lewis, G.R. / Coker, A.R. / Shoolingin-Jordan, P.M.
History
DepositionOct 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
C: 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)209,4318
Polymers209,1764
Non-polymers2554
Water28,4821581
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)104,6233
Polymers104,5882
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-14 kcal/mol
Surface area34540 Å2
MethodPISA
2
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8085
Polymers104,5882
Non-polymers2203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4610 Å2
ΔGint-14 kcal/mol
Surface area33880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.715, 133.566, 102.230
Angle α, β, γ (deg.)90.00, 104.98, 90.00
Int Tables number4
Space group name H-MP1211

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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: 52293.957 Da / Num. of mol.: 4 / Fragment: residues 40-520 / Source method: isolated from a natural source / Details: heart / Source: (natural) Sus scrofa (pig) / References: UniProt: Q29551, 3-oxoacid CoA-transferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1581 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4 ul Well Solution: 18-22% PEG 3350 or 4000, 75 mM Tris/HCl pH 8. 4 ul Protein solution: 10-15 mg/ml protein, 20 mM MOPS pH 7.2, 1 mM EDTA, 1 mM DTT, 0.2 mM PMSF, 10% glycerol, VAPOR ...Details: 4 ul Well Solution: 18-22% PEG 3350 or 4000, 75 mM Tris/HCl pH 8. 4 ul Protein solution: 10-15 mg/ml protein, 20 mM MOPS pH 7.2, 1 mM EDTA, 1 mM DTT, 0.2 mM PMSF, 10% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.948 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Jun 25, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 1.5→20 Å / Num. all: 297163 / Num. obs: 297163 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 17.16 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.042 / Net I/σ(I): 12
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 2.3 / Num. unique all: 18372 / Rsym value: 0.296 / % possible all: 82

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1O9L

1o9l


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.485 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18538 14899 5 %RANDOM
Rwork0.16502 ---
all0.1657 296782 --
obs0.1657 296782 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.924 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20.15 Å2
2---0.76 Å20 Å2
3----0.08 Å2
Refine analyzeLuzzati coordinate error obs: 0.238 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14137 0 14 1581 15732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214752
X-RAY DIFFRACTIONr_bond_other_d00.0210089
X-RAY DIFFRACTIONr_angle_refined_deg1.5281.97719997
X-RAY DIFFRACTIONr_angle_other_deg4.206324849
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20651964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.6824.817602
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.414152698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9021577
X-RAY DIFFRACTIONr_chiral_restr0.0970.22296
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216464
X-RAY DIFFRACTIONr_gen_planes_other0.0090.022801
X-RAY DIFFRACTIONr_nbd_refined0.220.22550
X-RAY DIFFRACTIONr_nbd_other0.2420.210168
X-RAY DIFFRACTIONr_nbtor_refined0.1770.27197
X-RAY DIFFRACTIONr_nbtor_other0.1110.27353
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2829
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.285
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3040.2306
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.2365
X-RAY DIFFRACTIONr_mcbond_it1.1141.512235
X-RAY DIFFRACTIONr_mcbond_other0.231.53891
X-RAY DIFFRACTIONr_mcangle_it1.208215095
X-RAY DIFFRACTIONr_scbond_it2.31536179
X-RAY DIFFRACTIONr_scangle_it3.2314.54848
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 910 -
Rwork0.225 17341 -
obs-17341 81.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6349-0.0283-0.06020.7053-0.08130.86360.02030.01990.07840.0379-0.0092-0.0459-0.1748-0.0432-0.0112-0.02550.0490.0022-0.12010.0103-0.158418.113766.918756.5878
23.23940.6332-0.01770.51450.22671.4694-0.0447-0.11350.0340.02090.0855-0.16110.03690.2971-0.0408-0.00890.0442-0.0354-0.0074-0.0115-0.030648.893868.018962.2421
30.5362-0.0896-0.04330.782-0.15410.8143-0.00570.042-0.084-0.03450.0036-0.04270.0794-0.04420.0021-0.07920.02680.0037-0.1162-0.0084-0.141220.541935.671455.7122
42.42830.4078-0.92041.3971-0.50682.6438-0.06240.2949-0.1003-0.10930.06130.25380.2113-0.41060.0011-0.07710.0033-0.00020.0185-0.0276-0.0659-9.923834.699865.1475
50.64920.03980.05280.97290.14640.6986-0.017-0.01370.0781-0.02040.02550.0229-0.08060.0279-0.0085-0.2093-0.0051-0.0055-0.1904-0.0066-0.14225.120273.85734.5221
62.60830.492-0.31811.60750.42051.73810.00810.07190.0512-0.08180.0325-0.245-0.12620.2223-0.0405-0.1899-0.0310.0037-0.0935-0.0077-0.056734.493477.38361.0751
70.7962-0.19310.03430.93710.1740.8349-0.0194-0.0654-0.11270.06160.02760.03010.13380.0247-0.0082-0.19260.0042-0.0015-0.18520.0024-0.13427.343442.81245.1388
82.5942-0.13240.10981.574-1.00893.3006-0.0713-0.396-0.20320.17130.19760.4220.2148-0.6889-0.1263-0.0929-0.05190.10490.09230.06340.0659-19.63842.520421.3651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 246
2X-RAY DIFFRACTION1A300 - 358
3X-RAY DIFFRACTION1A375 - 394
4X-RAY DIFFRACTION2A262 - 299
5X-RAY DIFFRACTION2A359 - 374
6X-RAY DIFFRACTION2A395 - 480
7X-RAY DIFFRACTION3B1 - 246
8X-RAY DIFFRACTION3B300 - 358
9X-RAY DIFFRACTION3B375 - 394
10X-RAY DIFFRACTION4B261 - 299
11X-RAY DIFFRACTION4B359 - 374
12X-RAY DIFFRACTION4B395 - 480
13X-RAY DIFFRACTION5C1 - 246
14X-RAY DIFFRACTION5C300 - 358
15X-RAY DIFFRACTION5C375 - 394
16X-RAY DIFFRACTION6C261 - 299
17X-RAY DIFFRACTION6C359 - 374
18X-RAY DIFFRACTION6C395 - 480
19X-RAY DIFFRACTION7D1 - 246
20X-RAY DIFFRACTION7D300 - 358
21X-RAY DIFFRACTION7D375 - 394
22X-RAY DIFFRACTION8D262 - 299
23X-RAY DIFFRACTION8D359 - 374
24X-RAY DIFFRACTION8D395 - 480

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