SAXSdb — 2nud

▼

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

Avirulence B protein

Pseudomonas syringae pv. glycinea

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	RPM1-interacting protein 4 × 1 （Q8GYN5） 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 TRIFLUOROETHANOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	RPM1-interacting protein 4 × 1 （Q8GYN5） 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 TRIFLUOROETHANOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AVRB_PSESG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–323； UniProt 1–321 Author chain B； PDBConstruct 3–323； UniProt 1–321

RPM1-interacting protein 4

OrganismNot specified

UniProt Q8GYN5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Avirulence B protein × 1 （P13835） 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 TRIFLUOROETHANOL × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Avirulence B protein × 1 （P13835） 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 TRIFLUOROETHANOL × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIN4_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–35； UniProt 142–176 Author chain D； PDBConstruct 1–35； UniProt 142–176

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2nud
Deposition date deposition_date	2006-11-09
Structure title title	The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide
Keywords keywords	AvrB RIN4 high-affinity crystal structure, TOXIN-PROTEIN BINDING COMPLEX; TOXIN/PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2nud__assembly_1__model_1

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

Download this curve (.dat)

2nud__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nud__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.27 Å
Rg (electron density)	20.25 Å
Total Rg	21.10 Å
Atom count	2530
Residues	314
Excluded volume	44297 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nud__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nud__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Avirulence B protein
Molecular weight formula_weight	36181.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5377

GAMGCVSSKSTTVLSPQTSFNEASRTSFRALPGPSQRQLEVYDQCLIGAARWPDDSSKSNTPENRAYCQSMYNSIRSAGDEISRGGITSFEELWGRATEWRLSKLQRGEPLYSAFASERTSDTDAVTPLVKPYKSVLARVVDHEDAHDEIMQDNLFGDLNVKVYRQTAYLHGNVIPLNTFRVATDTEYLRDRVAHLRTELGAKALKQHLQRYNPDRIDHTNASYLPIIKDHLNDLYRQAISSDLSQAELISLIARTHWWAASAMPDQRGSAAKAEFAARAIASAHGIELPPFRNGNVSDIEAMLSGEEEFVEKYRSLLDSDCF

Source Source

Source organism organism	Pseudomonas syringae pv. glycinea
NCBI taxonomy ID ncbi_taxonomy_id	318
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RPM1-interacting protein 4
Molecular weight formula_weight	4068.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

PEKVTVVPKFGDWDENNPSSADGYTHIFNKVREER

Entity 3 Entity 3 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	TRIFLUOROETHANOL
Molecular weight formula_weight	100.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	321

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2nuda1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.45 — Antivirulence factor
Superfamily Superfamily superfamily	e.45.1 — Antivirulence factor
Family Family family	e.45.1.1 — Antivirulence factor

Domain ID domain_id	d2nudb1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.45 — Antivirulence factor
Superfamily Superfamily superfamily	e.45.1 — Antivirulence factor
Family Family family	e.45.1.1 — Antivirulence factor

CATH v4.4 (2 domains)

Domain ID domain_id	2nudA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2nudB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	3290 — Fic-like fold
Homologous superfamily homologous superfamily	20 —

▶

Unit-cell length a length_a	45.884 Å
Unit-cell length b length_b	58.166 Å
Unit-cell length c length_c	119.767 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.92 °
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	2.300 Å
Low-resolution limit resolution_low	19.960 Å
R factor r_factor	0.2100
R_work r_work	0.2100
R_free r_free	0.2600

The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide

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

Avirulence B protein

State in the Current Structure

Other States of the Same Protein in the Database

RPM1-interacting protein 4

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

2nud__assembly_1__model_1

2nud__assembly_1__model_1 | I(q)

2nud__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The structure of the type III effector AvrB complexed with a high-affinity RIN4 peptide

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

Avirulence B 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

RPM1-interacting protein 4

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

2nud__assembly_1__model_1

2nud__assembly_1__model_1 | I(q)

2nud__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

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)