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- PDB-9xmy: Crystal structure of ASCT D62N mutant from Trypanosoma brucei in ... -

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Basic information

Entry
Database: PDB / ID: 9xmy
TitleCrystal structure of ASCT D62N mutant from Trypanosoma brucei in complex with succinyl-CoA and acetylacetone.
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 catabolic process / ketone body metabolic process / CoA-transferase activity / 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
ACETOACETIC ACID / SUCCINYL-COENZYME A / Succinyl-CoA:3-ketoacid-coenzyme A transferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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: Protein Sci. / Year: 2026
Title: Modulation of succinyl-CoA:3-ketoacid CoA transferase activity by a single amino acid residue in acetate:succinate CoA transferase from Trypanosoma brucei, the causative agent of African sleeping sickness.
Authors: Mochizuki, K. / Inaoka, D.K. / Fukuda, K. / Kurasawa, H. / Iyoda, K. / Nakai, U. / Harada, S. / Balogun, E.O. / Bringaud, F. / Boshart, M. / Sakura, T. / Hirayama, K. / Kita, K. / Shiba, T.
History
DepositionNov 11, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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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)214,83512
Polymers212,7354
Non-polymers2,1008
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.222, 164.833, 189.395
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: 53183.742 Da / Num. of mol.: 4 / Mutation: D62N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb11.02.0290 / Production host: Escherichia coli (E. coli) / References: UniProt: Q386P1, 3-oxoacid CoA-transferase
#2: Chemical ChemComp-AAE / ACETOACETIC ACID


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SCA / SUCCINYL-COENZYME A


Mass: 867.607 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H40N7O19P3S / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 46.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.05M HEPES-NAOH BUFFER, 18% (W/V) PEG 3350, 0.35M CACL2
PH range: 7.0-7.5

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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: Jul 22, 2022
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 59146 / % possible obs: 99.1 % / Redundancy: 6.6 % / CC1/2: 0.997 / Net I/σ(I): 12.6
Reflection shellResolution: 2.6→2.75 Å / Num. unique obs: 9350 / CC1/2: 0.897 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.865 / SU B: 17.422 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29575 2968 5.1 %RANDOM
Rwork0.20737 ---
obs0.21182 55724 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.989 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2---0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14193 0 128 71 14392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01214557
X-RAY DIFFRACTIONr_bond_other_d0.0010.01614068
X-RAY DIFFRACTIONr_angle_refined_deg1.631.81119708
X-RAY DIFFRACTIONr_angle_other_deg0.5581.75132315
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75251879
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.9275105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.362102445
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.22251
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217316
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023254
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_it3.744.8637537
X-RAY DIFFRACTIONr_mcbond_other3.7394.8637537
X-RAY DIFFRACTIONr_mcangle_it5.8228.7379409
X-RAY DIFFRACTIONr_mcangle_other5.8228.7379410
X-RAY DIFFRACTIONr_scbond_it4.3095.4347020
X-RAY DIFFRACTIONr_scbond_other4.3085.4347019
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8459.83210300
X-RAY DIFFRACTIONr_long_range_B_refined9.19846.6815303
X-RAY DIFFRACTIONr_long_range_B_other9.19846.6915302
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.664 Å
RfactorNum. reflection% reflection
Rfree0.386 213 -
Rwork0.337 3943 -
obs--98.18 %

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