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- PDB-6lp1: Crystal structure of acetate:succinate CoA transferase (ASCT) fro... -

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Basic information

Entry
Database: PDB / ID: 6lp1
TitleCrystal structure of acetate:succinate CoA transferase (ASCT) from Trypanosoma brucei.
ComponentsSuccinyl-CoA:3-ketoacid-coenzyme A transferase
KeywordsTRANSFERASE / Trypanosoma brucei / acetate:succinate CoA transferase / mitochondrial enzyme
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-CoA:3-ketoacid-coenzyme A transferase / Succinyl-CoA:3-ketoacid-coenzyme A transferase
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsMochizuki, K. / Inaoka, D.K. / Shiba, T. / Fukuda, K. / Kurasawa, H. / Mazet, M. / Millerioux, Y. / Bringaud, F. / Boshart, M. / Balogun, E.O. ...Mochizuki, K. / Inaoka, D.K. / Shiba, T. / Fukuda, K. / Kurasawa, H. / Mazet, M. / Millerioux, Y. / Bringaud, F. / Boshart, M. / Balogun, E.O. / Harada, S. / Hirayama, K. / Kita, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP18fm0208027 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16K19114, 23570131 , 26234567 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)16811362 , 19H03436 , 19K07523 Japan
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: The ASCT/SCS cycle fuels mitochondrial ATP and acetate production in Trypanosoma brucei.
Authors: Mochizuki, K. / Inaoka, D.K. / Mazet, M. / Shiba, T. / Fukuda, K. / Kurasawa, H. / Millerioux, Y. / Boshart, M. / Balogun, E.O. / Harada, S. / Hirayama, K. / Bringaud, F. / Kita, K.
History
DepositionJan 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)207,77710
Polymers207,4334
Non-polymers3456
Water6,666370
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)59.886, 164.635, 187.573
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 / acetate:succinate CoA transferase


Mass: 51858.133 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Variant: ILtat 1.4 / Production host: Escherichia coli (E. coli)
References: UniProt: D0A680, UniProt: Q386P1*PLUS, 3-oxoacid CoA-transferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Source detailsProtein crystallized and deposited in this structure is derived from Trypanosoma brucei ILtat 1.4 ...Protein crystallized and deposited in this structure is derived from Trypanosoma brucei ILtat 1.4 strain, which is not available at the time of data processing. Database D0A680 is dereived from Trypanosoma brucei gambiense (strain MHOM/CI/86/DAL972).

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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: 2.22 Å3/Da / Density % sol: 44.71 %
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: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 123547 / % possible obs: 98.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 31.4 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.107 / Net I/σ(I): 11.3
Reflection shellResolution: 2.01→2.13 Å / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 37706 / CC1/2: 0.698 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DLX

3dlx


Resolution: 2.01→19.97 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.187 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27867 6345 5.2 %RANDOM
Rwork0.22517 ---
obs0.22797 116411 98.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å2-0 Å2-0 Å2
2--0.03 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 2.01→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14070 0 16 370 14456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914339
X-RAY DIFFRACTIONr_bond_other_d0.0020.0213947
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.96419402
X-RAY DIFFRACTIONr_angle_other_deg1.019332026
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.49251867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.52924.335609
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.059152426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3991596
X-RAY DIFFRACTIONr_chiral_restr0.0940.22218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02116473
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023169
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_it1.5943.1477482
X-RAY DIFFRACTIONr_mcbond_other1.5943.1477481
X-RAY DIFFRACTIONr_mcangle_it2.5474.719343
X-RAY DIFFRACTIONr_mcangle_other2.5474.719344
X-RAY DIFFRACTIONr_scbond_it1.5693.3466857
X-RAY DIFFRACTIONr_scbond_other1.5693.3466857
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5294.94810060
X-RAY DIFFRACTIONr_long_range_B_refined4.324.48315590
X-RAY DIFFRACTIONr_long_range_B_other4.324.48315590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 483 -
Rwork0.27 8322 -
obs--97.54 %

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