Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT bound to coenzyme A in a hexamer state

Method: ELECTRON MICROSCOPY D_max: 81.1 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9y7v
deposition_date	2025-09-11
title	Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT bound to coenzyme A in a hexamer state
keywords	hexamer dihydrolipoamide acetyltransferase Mycobacterium tuberculosis Coenzyme A, TRANSFERASE; TRANSFERASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	27.99 Å
rg_electron	26.58 Å
i0	110475000.00
molecular_weight	80052.0 kDa
excluded_volume	99486 Å³
envelope_volume	128480 Å³
shell_volume	38992 Å³
envelope_diameter	85.1 Å
shell_rg	35.26 Å
envelope_rg	26.38 Å
shape_rg	26.58 Å
total_rg	27.46 Å
total_atoms	5625
n_residues	723
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

▼

3. P(r) Analysis (GNOM)

dmax	81.1 Å
rg_real	27.75 Å
rg_real_error	0.43 Å
i0_real	1.1050e+08
i0_real_error	1.3970e+06
rg_reciprocal	27.83 Å
i0_reciprocal	110500000.0000
total_estimate	0.9104
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	37.0 Å
skewness	0.070
kurtosis	-0.547
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	29170000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.969

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	4.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.20 Å
resolution_method	—
num_particles	35618

description	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
formula_weight	57146.4 kDa
ec_number	2.3.1.12
src_method	man
entity_count	3

Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT bound to coenzyme A in a hexamer state

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Mycobacterium tuberculosis
ncbi_taxonomy_id	1773
host_organism	Escherichia coli BL21

description	COENZYME A
formula_weight	767.5 kDa
src_method	syn
entity_count	3

fit	/app/data/saxs_computation/y7/9y7v/9y7v.fit
pddf	/app/data/pr_computation/y7/9y7v/9y7v.pr.out
profile	/app/data/saxs_computation/y7/9y7v/9y7v.dat

type	polypeptide(L)
strand_id	D,E,F
atom_count	5625