SAXSdb — 6aci

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

T3SS secreted effector NleB homolog

Escherichia coli O127:H6

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	FAS-associated death domain protein × 1 （Q13158） URIDINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B7UI21_ECO27
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–306； UniProt 28–329

FAS-associated death domain protein

Homo sapiens

UniProt Q13158

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	T3SS secreted effector NleB homolog × 1 （B7UI21） URIDINE-5'-DIPHOSPHATE × 1 MANGANESE (II) ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FADD_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 1–92； UniProt 93–184

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	6aci
Deposition date deposition_date	2018-07-26
Structure title title	Crystal structure of EPEC effector NleB in complex with FADD death domain
Keywords keywords	toxin, glycosyltransferase; TOXIN
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.

6aci__assembly_1__model_1

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

Download this curve (.dat)

6aci__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6aci__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.39 Å
Rg (electron density)	21.26 Å
Total Rg	22.15 Å
Atom count	3194
Residues	391
Excluded volume	56466 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6aci__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	T3SS secreted effector NleB homolog
Molecular weight formula_weight	35105.4 kDa
Mutation mutation	K115A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3630

SGRPSFAGKEYSLEPIDERTPILFQWFEARPERYEKGEVPILNTKEHPYLSNIINAAKIENERIIGVLVDGNFTYEQKKEFLNLENEHQNIAIIYRADVDFSMYDKKLSDIYLENIHKQESYPASERDNYLLGLLREELKNIPEGKDSLIESYAEKREHTWFDFFRNLAILKAGSLFTETGKTGCHNISPCSGCIYLDADMIITDKLGVLYAPDGIAVHVDCNDEIKSLENGAIVVNRSNHPALLAGLDIMKSKVDAHPYYDGLGKGIKRHFNYSSLHNYNAFCDFIEFKHENIIPNTSMYTSSSW

Source Source

Source organism organism	Escherichia coli O127:H6
NCBI taxonomy ID ncbi_taxonomy_id	574521
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	FAS-associated death domain protein
Molecular weight formula_weight	10614.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

GEEDLCAAFNVICDNVGKDWRRLARQLKVSDTKIDSIEDRYPRNLTERVRESLRIWKNTEKENATVAHLVGALRSCQMNLVADLVQEVQQAR

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	URIDINE-5'-DIPHOSPHATE
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	436

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6acih_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.2 — DEATH domain, DD

CATH v4.4 (1 domains)

Domain ID domain_id	6aciH00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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Unit-cell length a length_a	84.590 Å
Unit-cell length b length_b	84.590 Å
Unit-cell length c length_c	145.881 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	36.589 Å
R factor r_factor	0.1666
R_work r_work	0.1644
R_free r_free	0.2094

Crystal structure of EPEC effector NleB in complex with FADD death domain

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

T3SS secreted effector NleB homolog

State in the Current Structure

Other States of the Same Protein in the Database

FAS-associated death domain protein

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

6aci__assembly_1__model_1

6aci__assembly_1__model_1 | I(q)

6aci__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of EPEC effector NleB in complex with FADD death domain

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

T3SS secreted effector NleB homolog

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

FAS-associated death domain protein

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

6aci__assembly_1__model_1

6aci__assembly_1__model_1 | I(q)

6aci__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)