SAXSdb — 2dyj

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

Ribosome-binding factor A

Thermus thermophilus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5SJV1_THET8
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 1–95 Author chain B； PDBConstruct 1–95； UniProt 1–95

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	2dyj
Deposition date deposition_date	2006-09-14
Structure title title	Crystal structure of ribosome-binding factor A from Thermus thermophilus HB8
Keywords keywords	;16S rRNA processing, 17S RNA, KH domain, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, RIBOSOMAL PROTEIN ;; RIBOSOMAL PROTEIN
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.

2dyj__assembly_1__model_1

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

Download this curve (.dat)

2dyj__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dyj__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	14.46 Å
Rg (electron density)	12.88 Å
Total Rg	14.24 Å
Atom count	734
Residues	91
Excluded volume	13145 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dyj__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dyj__assembly_2__model_1`	monomeric （1）	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)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dyja1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.7 — Ribosome-binding factor A, RbfA
Family Family family	d.52.7.1 — Ribosome-binding factor A, RbfA

Domain ID domain_id	d2dyjb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.52 — Alpha-lytic protease prodomain-like
Superfamily Superfamily superfamily	d.52.7 — Ribosome-binding factor A, RbfA
Family Family family	d.52.7.1 — Ribosome-binding factor A, RbfA

CATH v4.4 (2 domains)

Domain ID domain_id	2dyjA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

Domain ID domain_id	2dyjB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	300 — GMP Synthetase; Chain A, domain 3
Homologous superfamily homologous superfamily	20 — K homology (KH) domain

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Unit-cell length a length_a	28.426 Å
Unit-cell length b length_b	65.838 Å
Unit-cell length c length_c	43.173 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.18 °
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	1.840 Å
Low-resolution limit resolution_low	42.920 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2450

Description description	Ribosome-binding factor A
Molecular weight formula_weight	10875.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1572

Crystal structure of ribosome-binding factor A from Thermus thermophilus HB8

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

Ribosome-binding factor A

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

2dyj__assembly_1__model_1

2dyj__assembly_1__model_1 | I(q)

2dyj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Thermus thermophilus
NCBI taxonomy ID ncbi_taxonomy_id	300852
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	105

Crystal structure of ribosome-binding factor A from Thermus thermophilus HB8

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

Ribosome-binding factor A

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

2dyj__assembly_1__model_1

2dyj__assembly_1__model_1 | I(q)

2dyj__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)