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- PDB-3dlx: Crystal structure of human 3-oxoacid CoA transferase 1 -

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Basic information

Entry
Database: PDB / ID: 3dlx
TitleCrystal structure of human 3-oxoacid CoA transferase 1
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase 1
KeywordsTRANSFERASE / OXCT1 / SCOT / Succinyl-CoA:3-ketoacid-coenzyme A transferase 1 / Disease mutation / Mitochondrion / Transit peptide / Structural Genomics / Structural Genomics Consortium / SGC
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 catabolic process / CoA-transferase activity / ketone body catabolic process / response to xenobiotic stimulus => GO:0009410 / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus ...Utilization of Ketone Bodies / cellular ketone body metabolic process / 3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone catabolic process / CoA-transferase activity / ketone body catabolic process / response to xenobiotic stimulus => GO:0009410 / response to starvation / positive regulation of insulin secretion involved in cellular response to glucose stimulus / adipose tissue development / response to hormone / response to nutrient / response to activity / brain development / heart development / response to ethanol / mitochondrial matrix / mitochondrion / nucleoplasm / identical protein binding
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKavanagh, K.L. / Shafqat, N. / Yue, W.W. / Picaud, S. / Murray, J.W. / Maclean, E.M. / von Delft, F. / Roos, A.K. / Arrowsmith, C.H. / Wikstrom, M. ...Kavanagh, K.L. / Shafqat, N. / Yue, W.W. / Picaud, S. / Murray, J.W. / Maclean, E.M. / von Delft, F. / Roos, A.K. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of human 3-oxoacid CoA transferase 1.
Authors: Kavanagh, K.L. / Shafqat, N. / Yue, W.W. / Picaud, S. / Murray, J.W. / Maclean, E.M. / von Delft, F. / Roos, A.K. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A.M. / Bountra, C. / Oppermann, U.
History
DepositionJun 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 30, 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_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_ref_seq_dif.details / _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
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,7886
Polymers212,6034
Non-polymers1842
Water6,756375
1
A: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3943
Polymers106,3022
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-15.1 kcal/mol
Surface area33350 Å2
MethodPISA
2
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3943
Polymers106,3022
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-15.3 kcal/mol
Surface area32220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.956, 168.492, 95.322
Angle α, β, γ (deg.)90.00, 105.86, 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 / Somatic-type succinyl CoA:3-oxoacid CoA-transferase / Scot-S


Mass: 53150.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OXCT1, OXCT, SCOT / Plasmid: pNic-CTHF / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55809, 3-oxoacid CoA-transferase
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.21 Å3/Da / Density % sol: 44.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 25% PEG 3350, 0.2 M NaCl, 0.1 M Tris-HCl, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 9, 2008
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.2→48.11 Å / Num. all: 92253 / Num. obs: 92253 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.4
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.9 / Num. unique all: 13203 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1M3E

1m3e


Resolution: 2.2→48.11 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.701 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.257 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Extra density in the active site could not be interpreted and was left unmodelled.
RfactorNum. reflection% reflectionSelection details
Rfree0.22473 1302 1.4 %RANDOM
Rwork0.17821 ---
all0.17887 90754 --
obs0.17887 90754 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å2-1.34 Å2
2--0.48 Å20 Å2
3----1.33 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13833 0 12 375 14220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214093
X-RAY DIFFRACTIONr_bond_other_d0.0010.029361
X-RAY DIFFRACTIONr_angle_refined_deg1.5561.96919096
X-RAY DIFFRACTIONr_angle_other_deg0.966322940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98751852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7524.432555
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.143152317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1541575
X-RAY DIFFRACTIONr_chiral_restr0.090.22207
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022726
X-RAY DIFFRACTIONr_nbd_refined0.1910.22519
X-RAY DIFFRACTIONr_nbd_other0.1970.29848
X-RAY DIFFRACTIONr_nbtor_refined0.1720.26709
X-RAY DIFFRACTIONr_nbtor_other0.0870.27603
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2523
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2630.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1850.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0970.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7111.59484
X-RAY DIFFRACTIONr_mcbond_other0.1681.53826
X-RAY DIFFRACTIONr_mcangle_it1.099214677
X-RAY DIFFRACTIONr_scbond_it1.9335233
X-RAY DIFFRACTIONr_scangle_it2.8984.54418
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 86 -
Rwork0.234 6472 -
obs--94.76 %
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)
11.25790.21190.33551.3094-0.16492.4639-0.00320.1396-0.1217-0.1090.1136-0.10180.18570.1064-0.1104-0.18720.05910.0061-0.1287-0.0372-0.220226.479337.201-1.4549
23.658-0.04711.02042.921-1.00162.25260.1378-0.0893-0.60130.08280.15510.40260.592-0.5336-0.2930.0482-0.1022-0.00640.06680.0701-0.02577.96319.537314.3289
30.85080.36630.33831.64680.41522.4056-0.1166-0.0950.27930.0019-0.00860.3179-0.5431-0.59260.1252-0.02230.2194-0.01430.0424-0.029-0.0918.748660.46619.5129
42.22360.9615-0.09762.80120.62243.2077-0.0613-0.04210.5624-0.17220.2238-0.162-0.83930.4163-0.16250.3213-0.0539-0.0405-0.0686-0.08540.059134.325776.73096.6061
51.5031-0.38520.42221.7258-0.12821.86850.1126-0.04830.1117-0.0275-0.0401-0.4219-0.06870.2043-0.0725-0.2349-0.01550.0254-0.17320.0133-0.119146.60735.76647.9422
62.3786-0.9254-0.4874.0243-2.13324.21660.1087-0.23940.33820.47480.26430.486-0.6763-0.2883-0.373-0.12170.04280.1078-0.12630.0029-0.080121.044951.247850.1605
71.5895-0.09550.07582.0510.2121.9380.1661-0.2452-0.49260.05-0.05110.19370.4893-0.2416-0.115-0.053-0.0975-0.1107-0.14240.1221-0.021428.381610.782452.293
85.93080.12652.62263.49351.063.0610.33730.6805-1.2024-0.33150.1161-0.4220.71390.5347-0.45340.24550.1018-0.116-0.0475-0.09550.311847.923-3.573936.9749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA40 - 2972 - 259
2X-RAY DIFFRACTION1AA342 - 393304 - 355
3X-RAY DIFFRACTION2AA298 - 341260 - 303
4X-RAY DIFFRACTION2AA394 - 519356 - 481
5X-RAY DIFFRACTION3BB40 - 2852 - 247
6X-RAY DIFFRACTION3BB342 - 393304 - 355
7X-RAY DIFFRACTION4BB299 - 341261 - 303
8X-RAY DIFFRACTION4BB394 - 518356 - 480
9X-RAY DIFFRACTION5CC40 - 2852 - 247
10X-RAY DIFFRACTION5CC342 - 393304 - 355
11X-RAY DIFFRACTION6CC299 - 341261 - 303
12X-RAY DIFFRACTION6CC394 - 519356 - 481
13X-RAY DIFFRACTION7DD40 - 2862 - 248
14X-RAY DIFFRACTION7DD342 - 393304 - 355
15X-RAY DIFFRACTION8DD302 - 341264 - 303
16X-RAY DIFFRACTION8DD394 - 519356 - 481

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