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9xmy

Crystal structure of ASCT D62N mutant from Trypanosoma brucei in complex with succinyl-CoA and acetylacetone.

Method: X-RAY DIFFRACTION Dmax: 116.2 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Succinyl-CoA:3-ketoacid-coenzyme A transferase

Trypanosoma brucei brucei TREU927

UniProt Q386P1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–493 Chain B； UniProt 1–493 Chain C； UniProt 1–493 Chain D； UniProt 1–493 Mutation：D62N AAE ACETOACETIC ACID × 2 CA CALCIUM ION × 4 SCA SUCCINYL-COENZYME A × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.05M HEPES-NAOH BUFFER, 18% (W/V) PEG 3350, 0.35M CACL2 Resolution 2.60 Å R-free 0.296

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9XMY Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8I3Y Crystal structure of ASCT from Trypanosoma brucei in complex with Succinyl-CoA. Deposited 2023-01-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–492（483 aa）
Chain B 10–492（483 aa）
Chain C 10–492（483 aa）
Chain D 10–492（483 aa）
Not recorded SCA SUCCINYL-COENZYME A × 1 CA CALCIUM ION × 4 SIN SUCCINIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.05M HEPES-NAOH BUFFER, 18% (W/V) PEG 3350, 0.35M CaCl2
Resolution 2.40 Å R-free 0.251
8I40 Crystal structure of ASCT from Trypanosoma brucei in complex with CoA. Deposited 2023-01-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 10–492（483 aa）
Chain B 10–492（483 aa）
Chain C 10–492（483 aa）
Chain D 10–492（483 aa）
Not recorded COA COENZYME A × 2 ACT ACETATE ION × 1 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.05M HEPES-NAOH BUFFER PH 7.4, 18% (W/V) PEG 3350, 0.35M CaCl2
Resolution 2.79 Å R-free 0.284

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q386P1_TRYB2
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–493； UniProt 1–493 Author chain B； PDBConstruct 1–493； UniProt 1–493 Author chain C； PDBConstruct 1–493； UniProt 1–493 Author chain D； PDBConstruct 1–493； UniProt 1–493

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9xmy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9xmy
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9xmy
Deposition date deposition_date2025-11-11
最后修订 last_revision2026-02-04
Structure title titleCrystal structure of ASCT D62N mutant from Trypanosoma brucei in complex with succinyl-CoA and acetylacetone.
Keywords keywordsTrypanosoma brucei, Acetate:succinate CoA transferase, ELECTRON TRANSPORT; ELECTRON TRANSPORT
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier38.42 Å
Radius of gyration Rg (electron density) rg_electron37.61 Å
Forward intensity I(0) i0640290000.00
Molecular weight molecular_weight204520.0 kDa
Excluded volume excluded_volume255080 ų
Envelope volume envelope_volume325570 ų
Hydration-shell volume shell_volume67525 ų
Envelope diameter envelope_diameter123.5 Å
Shell Rg shell_rg47.12 Å
Envelope Rg envelope_rg37.47 Å
Shape Rg shape_rg37.61 Å
Total Rg total_rg38.09 Å
Total atoms total_atoms14321
Residues n_residues1885
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax116.2 Å
Rg (real space) rg_real38.16 Å
Rg uncertainty (real space) rg_real_error0.58 Å
I(0) (real space) i0_real6.4030e+08
I(0) uncertainty (real space) i0_real_error9.4520e+06
Rg (reciprocal space) rg_reciprocal38.33 Å
I(0) (reciprocal space) i0_reciprocal640400000.0000
Solution quality estimate total_estimate0.9089
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary48.2 Å
Skewness Skewness skewness0.080
Kurtosis Kurtosis kurtosis-0.636
Angular range angular_range— – 0.2050 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha129700000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.961; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.946
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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8. Citations (1)

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9. Files and Curves (10)