SAXSdb — 4yxa

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

Surface presentation of antigens protein SpaO

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Oxygen-regulated invasion protein OrgB,Endolysin × 1 （P00720,P0CL45） water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Oxygen-regulated invasion protein OrgB,Endolysin × 1 （P00720,P0CL45） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPAO_SALTY
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 5–73； UniProt 145–213 Author chain D； PDBConstruct 5–73； UniProt 145–213 Author chain B； PDBConstruct 5–70； UniProt 232–297 Author chain E； PDBConstruct 5–70； UniProt 232–297

Oxygen-regulated invasion protein OrgB,Endolysin

Enterobacteria phage T4

UniProt P00720

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Surface presentation of antigens protein SpaO × 1 （P40699） Surface presentation of antigens protein SpaO × 1 （P40699） water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Surface presentation of antigens protein SpaO × 1 （P40699） Surface presentation of antigens protein SpaO × 1 （P40699） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ENLYS_BPT4
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 35–197； UniProt 2–164 Author chain F； PDBConstruct 35–197； UniProt 2–164

Oxygen-regulated invasion protein OrgB,Endolysin

Enterobacteria phage T4

UniProt P0CL45

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Surface presentation of antigens protein SpaO × 1 （P40699） Surface presentation of antigens protein SpaO × 1 （P40699） water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Surface presentation of antigens protein SpaO × 1 （P40699） Surface presentation of antigens protein SpaO × 1 （P40699） water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ORGB_SALTY
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 5–34； UniProt 1–30 Author chain F； PDBConstruct 5–34； UniProt 1–30

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	4yxa
Deposition date deposition_date	2015-03-22
Structure title title	Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein
Keywords keywords	Type III Secretion System, PROTEIN TRANSPORT; PROTEIN 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.

4yxa__assembly_1__model_1

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

Download this curve (.dat)

4yxa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4yxa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.47 Å
Rg (electron density)	21.54 Å
Total Rg	22.41 Å
Atom count	2318
Residues	294
Excluded volume	41714 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4yxa__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4yxa__assembly_2__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Surface presentation of antigens protein SpaO
Molecular weight formula_weight	8246.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	4940

GPVDPKMLRWPLRFVIGSSDTQRSLLGRIGIGDVLLIRTSRAEVYCYAKKLGHFNRVEGGIIVETLDIQHIEE

Source Source

Source organism organism	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
NCBI taxonomy ID ncbi_taxonomy_id	99287
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Surface presentation of antigens protein SpaO
Molecular weight formula_weight	7851.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

GPVDVKLEFVLYRKNVTLAELEAMGQQQLLSLPTNAELNVEIMANGVLLGNGELVQMNDTLGVEIHEWLS

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	99287
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Oxygen-regulated invasion protein OrgB,Endolysin
Molecular weight formula_weight	22162.6 kDa
EC 编号 ec_number	3.2.1.17
Mutation mutation	D20N, C54T, C97A,D20N, C54T, C97A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

GPVDMLKNIPIPSPLSPVEGILIKRKTLERYFSINIFEMLRIDEGLRLKIYKNTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDAYAAA

Source Source

Source organism organism	Enterobacteria phage T4
NCBI taxonomy ID ncbi_taxonomy_id	10665
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4yxaB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily	10 — SpoA-like

Domain ID domain_id	4yxaC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4yxaE00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	330 — Surface presentation of antigens (SPOA)
Homologous superfamily homologous superfamily	10 — SpoA-like

Domain ID domain_id	4yxaF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	62.880 Å
Unit-cell length b length_b	88.500 Å
Unit-cell length c length_c	63.320 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	116.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	45.804 Å
R factor r_factor	0.2027
R_work r_work	0.1984
R_free r_free	0.2618

Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein

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

Surface presentation of antigens protein SpaO

State in the Current Structure

Other States of the Same Protein in the Database

Oxygen-regulated invasion protein OrgB,Endolysin

State in the Current Structure

Other States of the Same Protein in the Database

Oxygen-regulated invasion protein OrgB,Endolysin

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

4yxa__assembly_1__model_1

4yxa__assembly_1__model_1 | I(q)

4yxa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Complex of SpaO(SPOA1,2 SeMet) and OrgB(APAR)::T4lysozyme fusion protein

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

Surface presentation of antigens protein SpaO

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Oxygen-regulated invasion protein OrgB,Endolysin

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Oxygen-regulated invasion protein OrgB,Endolysin

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

4yxa__assembly_1__model_1

4yxa__assembly_1__model_1 | I(q)

4yxa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)