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- PDB-8i3y: Crystal structure of ASCT from Trypanosoma brucei in complex with... -

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Basic information

Entry
Database: PDB / ID: 8i3y
TitleCrystal structure of ASCT from Trypanosoma brucei in complex with Succinyl-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
SUCCINYL-COENZYME A / SUCCINIC ACID / Succinyl-CoA:3-ketoacid-coenzyme A transferase
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 ASCT from Trypanosoma brucei in complex with Succinyl-CoA.
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

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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
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)208,69711
Polymers207,4334
Non-polymers1,2647
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.801, 163.654, 186.943
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 TREU927 (eukaryote)
Gene: Tb11.02.0290 / Production host: Escherichia coli (E. coli) / References: UniProt: Q386P1, 3-oxoacid CoA-transferase
#2: Chemical ChemComp-SCA / SUCCINYL-COENZYME A


Mass: 867.607 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H40N7O19P3S / 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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.28 Å3/Da / Density % sol: 46.12 %
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

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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: Jun 8, 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: 2.4→50 Å / Num. obs: 72921 / % possible obs: 99.7 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.128 / Rpim(I) all: 0.138 / Net I/σ(I): 12.8
Reflection shellResolution: 2.4→2.54 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 11459 / CC1/2: 0.851 / Rpim(I) all: 0.779 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→19.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.911 / SU B: 9.367 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.509 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24815 3585 4.9 %RANDOM
Rwork0.1916 ---
obs0.19439 68938 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.4→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14033 0 75 120 14228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914328
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213905
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9719392
X-RAY DIFFRACTIONr_angle_other_deg1.053331928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74551856
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41224.295603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.785152412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.761596
X-RAY DIFFRACTIONr_chiral_restr0.1020.22213
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02116432
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023161
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_it2.8554.3327448
X-RAY DIFFRACTIONr_mcbond_other2.8554.3327447
X-RAY DIFFRACTIONr_mcangle_it4.4756.4889296
X-RAY DIFFRACTIONr_mcangle_other4.4746.4889297
X-RAY DIFFRACTIONr_scbond_it3.0864.76880
X-RAY DIFFRACTIONr_scbond_other3.0834.6996878
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8866.91910096
X-RAY DIFFRACTIONr_long_range_B_refined7.07833.72415092
X-RAY DIFFRACTIONr_long_range_B_other7.07933.72815090
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 248 -
Rwork0.273 4956 -
obs--99.96 %

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