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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 D_max: 116.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xmy
deposition_date	2025-11-11
last_revision	2026-02-04
title	Crystal structure of ASCT D62N mutant from Trypanosoma brucei in complex with succinyl-CoA and acetylacetone.
keywords	Trypanosoma brucei, Acetate:succinate CoA transferase, ELECTRON TRANSPORT; ELECTRON TRANSPORT
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	38.42 Å
rg_electron	37.61 Å
i0	640290000.00
molecular_weight	204520.0 kDa
excluded_volume	255080 Å³
envelope_volume	325570 Å³
shell_volume	67525 Å³
envelope_diameter	123.5 Å
shell_rg	47.12 Å
envelope_rg	37.47 Å
shape_rg	37.61 Å
total_rg	38.09 Å
total_atoms	14321
n_residues	1885
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	116.2 Å
rg_real	38.16 Å
rg_real_error	0.58 Å
i0_real	6.4030e+08
i0_real_error	9.4520e+06
rg_reciprocal	38.33 Å
i0_reciprocal	640400000.0000
total_estimate	0.9089
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	48.2 Å
skewness	0.080
kurtosis	-0.636
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	129700000.0000
n_real_points	42
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Succinyl-CoA:3-ketoacid-coenzyme A transferase
formula_weight	53183.7 kDa
ec_number	2.8.3.5
mutation	D62N
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14398

MLRRTNFFRIGLDKVMSLSSAVQDIKNGATLAVGGFGTGGMPHAIMQEIKKMGVRDLIIYSNGAGVDGYGIGVLFENKQINKMIVSYVGNNKIFARQYLEGDVELEFCPQGSLAERMRAGGAGIPAFYTPTAVGTVLQTGGQITKYDKNGGVLKESTPRETRFFGGRLYCLENAIKTDFSIVKAWKGDRCGNLVFRGTARNFNVPVGQCGQTVIAEVENLVENGDIDPDEVHLPGVYVDRVVVPERYQTLIEHRTVTRHDGAGNKPTKASTRGEEVRQRIARRAALEFANGMYVNLGIGIPTESSNYIPAGVNVVLQSENGLIGMGPFPTEDKVDADWINAGKQTISHLAGSALFDSATSFAMIRGGHMDLTMLGALEVAANGDLANFMIPGKLVKGPGGAMDLVSCGTRVVVTTTHCNKNGDPKIVERCRLPVTGKHCVCRIITEYAVFDVVDGRLVLKEIAEDTTVDQVKKLTGVGFDADNVITMPLAPLT

Source

organism	Trypanosoma brucei brucei TREU927
common_name	Trypanosoma brucei brucei (strain 927/4 GUTat10.1)
ncbi_taxonomy_id	185431
host_organism	Escherichia coli

Entity 2 non-polymer

description	ACETOACETIC ACID
formula_weight	102.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SUCCINYL-COENZYME A
formula_weight	867.6 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	69

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6. Citations (1)

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length_a	60.222 Å
length_b	164.833 Å
length_c	189.395 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.600 Å
resolution_low	20.000 Å
r_factor	0.2118
r_work	0.2074
r_free	0.2958

fit	/app/data/saxs_computation/xm/9xmy/9xmy.fit
pddf	/app/data/pr_computation/xm/9xmy/9xmy.pr.out
profile	/app/data/saxs_computation/xm/9xmy/9xmy.dat