SAXSdb — 9y7v

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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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 1–553 Chain E； UniProt 1–553 Chain F； UniProt 1–553	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

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 9Y7V	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Y6T Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT in a hexamer state Deposited 2025-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	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）	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 2.65 Å
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 ligand/ion 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

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 D； PDBConstruct 1–553； UniProt 1–553 Author chain E； PDBConstruct 1–553； UniProt 1–553 Author chain F； PDBConstruct 1–553； UniProt 1–553

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	9y7v
Deposition date deposition_date	2025-09-11
Structure title title	Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT bound to coenzyme A in a hexamer state
Keywords keywords	hexamer dihydrolipoamide acetyltransferase Mycobacterium tuberculosis Coenzyme A, 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	27.99 Å
Radius of gyration Rg (electron density) rg_electron	26.58 Å
Forward intensity I(0) i0	110475000.00
Molecular weight molecular_weight	80052.0 kDa
Excluded volume excluded_volume	99486 Å³
Envelope volume envelope_volume	128480 Å³
Hydration-shell volume shell_volume	38992 Å³
Envelope diameter envelope_diameter	85.1 Å
Shell Rg shell_rg	35.26 Å
Envelope Rg envelope_rg	26.38 Å
Shape Rg shape_rg	26.58 Å
Total Rg total_rg	27.46 Å
Total atoms total_atoms	5625
Residues n_residues	723
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	81.1 Å
Rg (real space) rg_real	27.75 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	1.1050e+08
I(0) uncertainty (real space) i0_real_error	1.3970e+06
Rg (reciprocal space) rg_reciprocal	27.83 Å
I(0) (reciprocal space) i0_reciprocal	110500000.0000
Solution quality estimate total_estimate	0.9104
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.0 Å
Skewness Skewness skewness	0.070
Kurtosis Kurtosis kurtosis	-0.547
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29170000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.965; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.969

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex
Molecular weight formula_weight	57146.4 kDa
EC 编号 ec_number	2.3.1.12
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F
Atom count atom_count	5625

MAFSVQMPALGESVTEGTVTRWLKQEGDTVELDEPLVEVSTDKVDTEIPSPAAGVLTKIIAQEDDTVEVGGELAVIGDAKDAGEAAAPAPEKVPAAQPESKPAPEPPPVQPTSGAPAGGDAKPVLMPELGESVTEGTVIRWLKKIGDSVQVDEPLVEVSTDKVDTEIPSPVAGVLVSISADEDATVPVGGELARIGVAADIGAAPAPKPAPKPVPEPAPTPKAEPAPSPPAAQPAGAAEGAPYVTPLVRKLASENNIDLAGVTGTGVGGRIRKQDVLAAAEQKKRAKAPAPAAQAAAAPAPKAPPAPAPALAHLRGTTQKASRIRQITANKTRESLQATAQLTQTHEVDMTKIVGLRARAKAAFAEREGVNLTFLPFFAKAVIDALKIHPNINASYNEDTKEITYYDAEHLGFAVDTEQGLLSPVIHDAGDLSLAGLARAIADIAARARSGNLKPDELSGGTFTITNIGSQGALFDTPILVPPQAAMLGTGAIVKRPRVVVDASGNESIGVRSVCYLPLTYDHRLIDGADAGRFLTTIKHRLEEGAFEADLGL

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	3

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

Resolution resolution	4.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	35618

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

Structure of Mycobacterium tuberculosis pyruvate dehydrogenase complex E2p core subunit DlaT bound to coenzyme A 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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)