SAXSdb — 2yjt

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

REGULATOR OF RIBONUCLEASE ACTIVITY A

ESCHERICHIA COLI

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	ATP-DEPENDENT RNA HELICASE SRMB × 1 （P21507） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D8AM26_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–161； UniProt 1–161 Author chain B； PDBConstruct 1–161； UniProt 1–161 Author chain C； PDBConstruct 1–161； UniProt 1–161

ATP-DEPENDENT RNA HELICASE SRMB

ESCHERICHIA COLI

UniProt P21507

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	REGULATOR OF RIBONUCLEASE ACTIVITY A × 3 （D8AM26） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SRMB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain D； PDBConstruct 1–170； UniProt 219–388

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	2yjt
Deposition date deposition_date	2011-05-23
Structure title title	Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)
Keywords keywords	HYDROLASE INHIBITOR-HYDROLASE COMPLEX, DEAD BOX RNA HELICASES; HYDROLASE INHIBITOR/HYDROLASE
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.

2yjt__assembly_1__model_1

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

Download this curve (.dat)

2yjt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yjt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.05 Å
Rg (electron density)	30.48 Å
Total Rg	31.02 Å
Atom count	4964
Residues	644
Excluded volume	87537 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yjt__assembly_1__model_1`	tetrameric （4）	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	REGULATOR OF RIBONUCLEASE ACTIVITY A
Molecular weight formula_weight	17371.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	4993

MKYDTSELCDIYQEDVNVVEPLFSNFGGRASFGGQIITVKCFEDNGLLYDLLEQNGRGRVLVVDGGGSVRRALVDAELARLAVQNEWEGLVIYGAVRQVDDLEELDIGIQAMAAIPVGAAGEGIGESDVRVNFGGVTFFSGDHLYADNTGIILSEDPLDIE

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	ATP-DEPENDENT RNA HELICASE SRMB
Molecular weight formula_weight	19559.5 kDa
EC 编号 ec_number	3.6.4.13
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

RKKIHQWYYRADDLEHKTALLVHLLKQPEATRSIVFVRKRERVHELANWLREAGINNCYLEGEMVQGKRNEAIKRLTEGRVNVLVATDVAARGIDIPDVSHVFNFDMPRSGDTYLHRIGRTARAGRKGTAISLVEAHDHLLLGKVGRYIEEPIKARVIDELRPKTRAPSE

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	29

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2yjta_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d2yjtb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d2yjtc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.7 — RraA-like
Family Family family	c.8.7.1 — RraA-like

Domain ID domain_id	d2yjtd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	2yjtA00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	2yjtB00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	2yjtC00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	30 — Glucose Oxidase; domain 1
Homologous superfamily homologous superfamily	40 — Ribonuclease E inhibitor RraA/RraA-like

Domain ID domain_id	2yjtD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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Unit-cell length a length_a	73.390 Å
Unit-cell length b length_b	73.390 Å
Unit-cell length c length_c	222.891 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	74.300 Å
R factor r_factor	0.1954
R_work r_work	0.1923
R_free r_free	0.2566

Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)

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

REGULATOR OF RIBONUCLEASE ACTIVITY A

State in the Current Structure

Other States of the Same Protein in the Database

ATP-DEPENDENT RNA HELICASE SRMB

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

2yjt__assembly_1__model_1

2yjt__assembly_1__model_1 | I(q)

2yjt__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of E. coli DEAD-box protein SrmB bound to regulator of ribonuclease activity A (RraA)

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

REGULATOR OF RIBONUCLEASE ACTIVITY 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

ATP-DEPENDENT RNA HELICASE SRMB

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

2yjt__assembly_1__model_1

2yjt__assembly_1__model_1 | I(q)

2yjt__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

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)