SAXSdb — 8gak

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

Lipopolysaccharide export system protein LptA

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Thanatin × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Thanatin × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Thanatin × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6D0DFJ5_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–132； UniProt 28–159 Author chain C； PDBConstruct 1–132； UniProt 28–159

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	8gak
Deposition date deposition_date	2023-02-23
Structure title title	Crystal Structure of E. coli LptA in complex with Chinavia Ubica Thanatin
Keywords keywords	LptA, Thanatin, ANTIBIOTIC, ANTIBIOTIC-LIPID TRANSPORT complex; ANTIBIOTIC/LIPID TRANSPORT
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.

8gak__assembly_3__model_1

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

Download this curve (.dat)

8gak__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8gak__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	19.35 Å
Rg (electron density)	19.29 Å
Total Rg	19.96 Å
Atom count	1103
Residues	147
Excluded volume	19463 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8gak__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8gak__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`8gak__assembly_3__model_1`	dimeric （2）	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	Lipopolysaccharide export system protein LptA
Molecular weight formula_weight	14536.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2384

VTGDTDQPIHIESDQQSLDMQGNVVTFTGNVIVTQGTIKINADKVVVTRPGGEQGKEVIDGYGKPATFYQMQDNGKPVEGHASQMHYELAKDFVVLTGNAYLQQVDSNIKGDKITYLVKEQKMQAFSDKGKR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Thanatin
Molecular weight formula_weight	2147.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GSKPVPIIACNRKTGKCTRI

Source Source

Source organism organism	Chinavia ubica
NCBI taxonomy ID ncbi_taxonomy_id	1497372
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	139

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Unit-cell length a length_a	45.510 Å
Unit-cell length b length_b	62.130 Å
Unit-cell length c length_c	150.080 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	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	47.860 Å
R factor r_factor	0.1996
R_work r_work	0.1975
R_free r_free	0.2395

Crystal Structure of E. coli LptA in complex with Chinavia Ubica Thanatin

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

Lipopolysaccharide export system protein LptA

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

8gak__assembly_3__model_1

8gak__assembly_3__model_1 | I(q)

8gak__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)

Crystal Structure of E. coli LptA in complex with Chinavia Ubica Thanatin

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

Lipopolysaccharide export system protein LptA

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

8gak__assembly_3__model_1

8gak__assembly_3__model_1 | I(q)

8gak__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

7. Citations (1)