SAXSdb — 2xd0

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

TOXN

PECTOBACTERIUM ATROSEPTICUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	TOXI × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	TOXI × 1 water × 2	Consistent with all polymers
3	Protein–RNA	Monomer	Protein 1 RNA 1	TOXI × 1 water × 2	Consistent with all polymers
4	Protein–RNA	Monomer	Protein 1 RNA 1	TOXI × 1 water × 2	Consistent with all polymers
5	Protein–RNA	Monomer	Protein 1 RNA 1	TOXI × 1 water × 2	Consistent with all polymers
6	Protein–RNA	Monomer	Protein 1 RNA 1	TOXI × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B8X8Z0_ERWCT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 1–171 Author chain B； PDBConstruct 1–171； UniProt 1–171 Author chain E； PDBConstruct 1–171； UniProt 1–171 Author chain X； PDBConstruct 1–171； UniProt 1–171 Author chain Y； PDBConstruct 1–171； UniProt 1–171 Author chain Z； PDBConstruct 1–171； UniProt 1–171

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	2xd0
Deposition date deposition_date	2010-04-28
Structure title title	A processed non-coding RNA regulates a bacterial antiviral system
Keywords keywords	TOXIN-RNA COMPLEX, ABORTIVE INFECTION, PHAGE; TOXIN/RNA
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.

2xd0__assembly_1__model_1

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

Download this curve (.dat)

2xd0__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2xd0__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.40 Å
Rg (electron density)	21.51 Å
Total Rg	22.17 Å
Atom count	2080
Residues	197
Excluded volume	34564 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2xd0__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2xd0__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2xd0__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2xd0__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2xd0__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2xd0__assembly_6__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	TOXN
Molecular weight formula_weight	19726.5 kDa
EC 编号 ec_number	3.1.27.3
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,E,X,Y,Z
Atom count atom_count	12651

MKFYTISSKYIEYLKEFDDKVPNSEDPTYQNPKAFIGIVLEIQGHKYLAPLTSPKKWHNNVKESSLSCFKLHENGVPENQLGLINLKFMIPIIEAEVSLLDLGNMPNTPYKRMLYKQLQFIRANSDKIASKSDTLRNLVLQGKMQGTCNFSLLEEKYRDFGKEAEDTEEGE

Source Source

Source organism organism	PECTOBACTERIUM ATROSEPTICUM
NCBI taxonomy ID ncbi_taxonomy_id	29471
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	TOXI
Molecular weight formula_weight	11575.8 kDa
Source method src_method	syn
Copy count entity_count	6

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G,H,I,U,V,W

AUUCAGGUGAUUUGCUACCUUUAAGUGCAGCUAGAA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2xd0A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2xd0B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2xd0E00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2xd0X00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2xd0Y00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	130 —

Domain ID domain_id	2xd0Z00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	129 — Thiol Ester Dehydrase; Chain A
Homologous superfamily homologous superfamily	130 —

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Unit-cell length a length_a	42.139 Å
Unit-cell length b length_b	119.125 Å
Unit-cell length c length_c	377.057 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	24

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

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	35.000 Å
R factor r_factor	0.2160
R_work r_work	0.2140
R_free r_free	0.2580

A processed non-coding RNA regulates a bacterial antiviral system

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

TOXN

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

2xd0__assembly_1__model_1

2xd0__assembly_1__model_1 | I(q)

2xd0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

A processed non-coding RNA regulates a bacterial antiviral system

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

TOXN

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

2xd0__assembly_1__model_1

2xd0__assembly_1__model_1 | I(q)

2xd0__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)