SAXSdb — 2czj

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

SsrA-binding protein

Thermus thermophilus

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	tmRNA (63-MER) × 1	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	tmRNA (63-MER) × 1	Consistent with all polymers
3	Protein–RNA	Monomer	Protein 1 RNA 1	tmRNA (63-MER) × 1	Consistent with all polymers
4	Protein–RNA	Monomer	Protein 1 RNA 1	tmRNA (63-MER) × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSRP_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 1–123 Author chain C； PDBConstruct 1–123； UniProt 1–123 Author chain E； PDBConstruct 1–123； UniProt 1–123 Author chain G； PDBConstruct 1–123； UniProt 1–123

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	2czj
Deposition date deposition_date	2005-07-13
Structure title title	Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8
Keywords keywords	;SmpB, tmRNA, SsrA RNA, 10Sa RNA, tRNA, trans-translation, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RNA BINDING PROTEIN-RNA COMPLEX ;; RNA BINDING PROTEIN/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.

2czj__assembly_3__model_1

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

Download this curve (.dat)

2czj__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2czj__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	22.84 Å
Rg (electron density)	22.02 Å
Total Rg	22.71 Å
Atom count	2316
Residues	182
Excluded volume	36598 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2czj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2czj__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2czj__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2czj__assembly_4__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 (2)

Entity 1 Entity 1 polymer

Description description	SsrA-binding protein
Molecular weight formula_weight	14177.5 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	9224

MAPVLENRRARHDYEILETYEAGIALKGTEVKSLRAGKVDFTGSFARFEDGELYLENLYIAPYEKGSYANVDPRRKRKLLLHKHELRRLLGKVEQKGLTLVPLKIYFNERGYAKVLLGLARGK

Source Source

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	tmRNA (63-MER)
Molecular weight formula_weight	20289.1 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B,D,F,H

GGGGGUGAAACGGUCUCGACAGGGGUUCGCCUUUGGACGUGGGUUCGACUCCCACCACCUCCA

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2czja1
Class class	b — All beta proteins
Fold Fold fold	b.111 — Small protein B (SmpB)
Superfamily Superfamily superfamily	b.111.1 — Small protein B (SmpB)
Family Family family	b.111.1.1 — Small protein B (SmpB)

Domain ID domain_id	d2czjc1
Class class	b — All beta proteins
Fold Fold fold	b.111 — Small protein B (SmpB)
Superfamily Superfamily superfamily	b.111.1 — Small protein B (SmpB)
Family Family family	b.111.1.1 — Small protein B (SmpB)

Domain ID domain_id	d2czje1
Class class	b — All beta proteins
Fold Fold fold	b.111 — Small protein B (SmpB)
Superfamily Superfamily superfamily	b.111.1 — Small protein B (SmpB)
Family Family family	b.111.1.1 — Small protein B (SmpB)

Domain ID domain_id	d2czjg1
Class class	b — All beta proteins
Fold Fold fold	b.111 — Small protein B (SmpB)
Superfamily Superfamily superfamily	b.111.1 — Small protein B (SmpB)
Family Family family	b.111.1.1 — Small protein B (SmpB)

CATH v4.4 (4 domains)

Domain ID domain_id	2czjA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	280 — Small Protein B; Chain: A;
Homologous superfamily homologous superfamily	10 — Small protein B

Domain ID domain_id	2czjC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	280 — Small Protein B; Chain: A;
Homologous superfamily homologous superfamily	10 — Small protein B

Domain ID domain_id	2czjE00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	280 — Small Protein B; Chain: A;
Homologous superfamily homologous superfamily	10 — Small protein B

Domain ID domain_id	2czjG00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	280 — Small Protein B; Chain: A;
Homologous superfamily homologous superfamily	10 — Small protein B

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Unit-cell length a length_a	84.776 Å
Unit-cell length b length_b	67.957 Å
Unit-cell length c length_c	178.662 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	3.010 Å
Low-resolution limit resolution_low	48.760 Å
R factor r_factor	—
R_work r_work	0.2550
R_free r_free	0.3200

Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8

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

SsrA-binding 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

2czj__assembly_3__model_1

2czj__assembly_3__model_1 | I(q)

2czj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of the tRNA domain of tmRNA from Thermus thermophilus HB8

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

SsrA-binding 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

2czj__assembly_3__model_1

2czj__assembly_3__model_1 | I(q)

2czj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)