SAXSdb — 9y6t

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

Mycobacterium tuberculosis

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 313–553 Chain B； UniProt 313–553 Chain C； UniProt 313–553 Chain D； UniProt 313–553 Chain E； UniProt 313–553 Chain F； UniProt 313–553	Not recorded	No other associated polymer	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；20 mM Tris, pH 7.5, 5 mM MgCl2, and 100 mM KCl cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.65 Å

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 9Y6T	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Y72 Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT in a two-hexamer state Deposited 2025-09-09	Different construct Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 313–553（241 aa） Chain B 313–553（241 aa） Chain C 313–553（241 aa） Chain D 313–553（241 aa） Chain E 313–553（241 aa） Chain F 313–553（241 aa） Chain G 313–553（241 aa） Chain H 313–553（241 aa） Chain I 313–553（241 aa） Chain J 313–553（241 aa） Chain K 313–553（241 aa） Chain L 313–553（241 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Tris, pH 7.5, 5 mM MgCl2, and 100 mM KCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.51 Å
9Y7V Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT bound to coenzyme A in a hexamer state Deposited 2025-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1–553（553 aa） Chain E 1–553（553 aa） Chain F 1–553（553 aa）	Not recorded	COA COENZYME A × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM Tris, pH 7.5, 5 mM MgCl2, and 100 mM KCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å

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

View Construct and Data Evidence

UniProt name	ODP2_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–241； UniProt 313–553 Author chain B； PDBConstruct 1–241； UniProt 313–553 Author chain C； PDBConstruct 1–241； UniProt 313–553 Author chain D； PDBConstruct 1–241； UniProt 313–553 Author chain E； PDBConstruct 1–241； UniProt 313–553 Author chain F； PDBConstruct 1–241； UniProt 313–553

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9y6t
Deposition date deposition_date	2025-09-09
Structure title title	Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT in a hexamer state
Keywords keywords	hexamer dihydrolipoamide acetyltransferase Mycobacterium tuberculosis pyruvate dehydrogenase complex, TRANSFERASE; TRANSFERASE
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	39.26 Å
Radius of gyration Rg (electron density) rg_electron	38.39 Å
Forward intensity I(0) i0	367607000.00
Molecular weight molecular_weight	155500.0 kDa
Excluded volume excluded_volume	194590 Å³
Envelope volume envelope_volume	250750 Å³
Hydration-shell volume shell_volume	53776 Å³
Envelope diameter envelope_diameter	120.0 Å
Shell Rg shell_rg	45.03 Å
Envelope Rg envelope_rg	37.86 Å
Shape Rg shape_rg	38.40 Å
Total Rg total_rg	38.71 Å
Total atoms total_atoms	10962
Residues n_residues	1446
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	123.8 Å
Rg (real space) rg_real	39.24 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	3.6760e+08
I(0) uncertainty (real space) i0_real_error	5.4390e+06
Rg (reciprocal space) rg_reciprocal	39.26 Å
I(0) (reciprocal space) i0_reciprocal	367600000.0000
Solution quality estimate total_estimate	0.8268
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.2 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.724
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	75220000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.650 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.65 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	379608

Description description	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Molecular weight formula_weight	25951.4 kDa
EC 编号 ec_number	2.3.1.12
Source method src_method	man
Copy count entity_count	6

Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT in a hexamer state

1. Protein Identity and Related Structures Protein Identity & Related Structures

Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10962

来源生物 organism	Mycobacterium tuberculosis
NCBI Class编号 ncbi_taxonomy_id	1773
宿主生物 host_organism	Escherichia coli BL21

fit	/app/data/saxs_computation/y6/9y6t/9y6t.fit
pddf	/app/data/pr_computation/y6/9y6t/9y6t.pr.out
profile	/app/data/saxs_computation/y6/9y6t/9y6t.dat