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- PDB-8i40: Crystal structure of ASCT from Trypanosoma brucei in complex with CoA. -

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Basic information

Entry
Database: PDB / ID: 8i40
TitleCrystal structure of ASCT from Trypanosoma brucei in complex with CoA.
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase
KeywordsELECTRON TRANSPORT / Trypanosoma brucei / Acetate:succinate CoA transferase
Function / homology
Function and homology information


3-oxoacid CoA-transferase / succinyl-CoA:3-oxo-acid CoA-transferase activity / ketone body metabolic process / CoA-transferase activity / ketone body catabolic process / mitochondrion / metal ion binding / cytoplasm
Similarity search - Function
3-oxoacid CoA-transferase / Coenzyme A transferase binding site / Coenzyme A transferases signature 1. / Coenzyme A transferase active site / Coenzyme A transferases signature 2. / 3-oxoacid CoA-transferase, subunit B / Coenzyme A transferase family I / Coenzyme A transferase / Coenzyme A transferase / NagB/RpiA transferase-like
Similarity search - Domain/homology
ACETATE ION / COENZYME A / Succinyl-CoA:3-ketoacid-coenzyme A transferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsMochizuki, K. / Inaoka, D.K. / Fukuda, K. / Kurasawa, H. / Iyoda, K. / Nakai, U. / Harada, S. / Balogun, E.O. / Mazet, M. / Millerioux, Y. ...Mochizuki, K. / Inaoka, D.K. / Fukuda, K. / Kurasawa, H. / Iyoda, K. / Nakai, U. / Harada, S. / Balogun, E.O. / Mazet, M. / Millerioux, Y. / Bringaud, F. / Boshart, M. / Hirayama, K. / Kita, K. / Shiba, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of ligand complexes of ASCT from Trypanosoma brucei and molecular mechanism in comparison with mammalian SCOT.
Authors: Mochizuki, K. / Inaoka, D.K. / Fukuda, K. / Kurasawa, H. / Iyoda, K. / Nakai, U. / Harada, S. / Balogun, E.O. / Mazet, M. / Millerioux, Y. / Bringaud, F. / Boshart, M. / Hirayama, K. / Kita, K. / Shiba, T.
History
DepositionJan 18, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
B: Succinyl-CoA:3-ketoacid-coenzyme A transferase
C: Succinyl-CoA:3-ketoacid-coenzyme A transferase
D: Succinyl-CoA:3-ketoacid-coenzyme A transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,18711
Polymers207,4334
Non-polymers1,7547
Water61334
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, CHAINS: A, B, C, D
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.789, 165.146, 188.584
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Succinyl-CoA:3-ketoacid-coenzyme A transferase


Mass: 51858.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (eukaryote)
Gene: Tb11.02.0290 / Production host: Escherichia coli (E. coli) / References: UniProt: Q386P1, 3-oxoacid CoA-transferase
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.05M HEPES-NAOH BUFFER PH 7.4, 18% (W/V) PEG 3350, 0.35M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 46801 / % possible obs: 98.6 % / Redundancy: 6.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.219 / Rpim(I) all: 0.219 / Net I/σ(I): 8.2
Reflection shellResolution: 2.79→2.96 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.739 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 7331 / CC1/2: 0.801 / Rpim(I) all: 0.811 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→19.9 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.841 / SU B: 19.787 / SU ML: 0.384 / Cross valid method: THROUGHOUT / ESU R Free: 0.458 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28406 2242 4.8 %RANDOM
Rwork0.2234 ---
obs0.22632 44447 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.877 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.79→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14060 0 104 34 14198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01914392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213948
X-RAY DIFFRACTIONr_angle_refined_deg1.281.97219485
X-RAY DIFFRACTIONr_angle_other_deg0.919332027
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68851860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1224.333607
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.641152416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1311596
X-RAY DIFFRACTIONr_chiral_restr0.0710.22221
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023176
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_it1.444.7347465
X-RAY DIFFRACTIONr_mcbond_other1.444.7347464
X-RAY DIFFRACTIONr_mcangle_it2.5147.0959316
X-RAY DIFFRACTIONr_mcangle_other2.5147.0969317
X-RAY DIFFRACTIONr_scbond_it1.1914.9036927
X-RAY DIFFRACTIONr_scbond_other1.1914.9036928
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.077.31110170
X-RAY DIFFRACTIONr_long_range_B_refined4.06336.55615042
X-RAY DIFFRACTIONr_long_range_B_other4.06336.55815043
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.792→2.863 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 160 -
Rwork0.305 3128 -
obs--96.37 %

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