SAXSdb — 2c8m

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

LIPOATE-PROTEIN LIGASE A

THERMOPLASMA ACIDOPHILUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	LIPOIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	LIPOIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	LIPOIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	LIPOIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LPLA_THEAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–262； UniProt 1–262 Author chain B； PDBConstruct 1–262； UniProt 1–262 Author chain C； PDBConstruct 1–262； UniProt 1–262 Author chain D； PDBConstruct 1–262； UniProt 1–262

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	2c8m
Deposition date deposition_date	2005-12-06
Structure title title	Structure of protein Ta0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid
Keywords keywords	LIPOYLATION, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2c8m__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2c8m__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2c8m__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.15 Å
Rg (electron density)	16.86 Å
Total Rg	17.80 Å
Atom count	1894
Residues	245
Excluded volume	33563 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2c8m__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2c8m__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2c8m__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2c8m__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	LIPOATE-PROTEIN LIGASE A
Molecular weight formula_weight	29915.3 kDa
EC 编号 ec_number	6.3.2.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8042

MEGRLLLLETPGNTRMSLAYDEAIYRSFQYGDKPILRFYRHDRSVIIGYFQVAEEEVDLDYMKKNGIMLARRYTGGGAVYHDLGDLNFSVVRSSDDMDITSMFRTMNEAVVNSLRILGLDARPGELNDVSIPVNKKTDIMAGEKKIMGAAGAMRKGAKLWHAAMLVHTDLDMLSAVLKVPDEKFRDKIAKSTRERVANVTDFVDVSIDEVRNALIRGFSETLHIDFREDTITEKEESLARELFDKKYSTEEWNMGLLRKEVV

Source Source

Source organism organism	THERMOPLASMA ACIDOPHILUM
NCBI taxonomy ID ncbi_taxonomy_id	273075
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	LIPOIC ACID
Molecular weight formula_weight	206.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	484

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2c8ma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.3 — LplA-like

Domain ID domain_id	d2c8mb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.3 — LplA-like

Domain ID domain_id	d2c8mc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.3 — LplA-like

Domain ID domain_id	d2c8md_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.104 — Class II aaRS and biotin synthetases
Superfamily Superfamily superfamily	d.104.1 — Class II aaRS and biotin synthetases
Family Family family	d.104.1.3 — LplA-like

CATH v4.4 (4 domains)

Domain ID domain_id	2c8mA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2c8mB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2c8mC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	2c8mD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

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Unit-cell length a length_a	53.377 Å
Unit-cell length b length_b	117.882 Å
Unit-cell length c length_c	105.663 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.51 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	53.300 Å
R factor r_factor	0.2080
R_work r_work	0.2070
R_free r_free	0.2390

Structure of protein Ta0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid

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

LIPOATE-PROTEIN LIGASE A

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2c8m__assembly_3__model_1

2c8m__assembly_3__model_1 | I(q)

2c8m__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of protein Ta0514, putative lipoate protein ligase from T. acidophilum with bound lipoic acid

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

LIPOATE-PROTEIN LIGASE A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2c8m__assembly_3__model_1

2c8m__assembly_3__model_1 | I(q)

2c8m__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)