2yjv

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

Method: X-RAY DIFFRACTION

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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 homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 3	water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RRAA_ECOLI
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 Author chain D； PDBConstruct 1–161； UniProt 1–161 Author chain E； PDBConstruct 1–161； UniProt 1–161 Author chain F； PDBConstruct 1–161； UniProt 1–161 Author chain G； PDBConstruct 1–161； UniProt 1–161 Author chain H； PDBConstruct 1–161； UniProt 1–161 Author chain I； PDBConstruct 1–161； UniProt 1–161 Author chain J； PDBConstruct 1–161； UniProt 1–161 Author chain K； PDBConstruct 1–161； UniProt 1–161 Author chain L； PDBConstruct 1–161； UniProt 1–161

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	2yjv
Deposition date deposition_date	2011-05-24
Structure title title	Crystal structure of E. coli regulator of ribonuclease activity A (RraA) bound to fragment of DEAD-box protein RhlB
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.

2yjv__assembly_1__model_1

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

Download this curve (.dat)

2yjv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yjv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.09 Å
Rg (electron density)	23.91 Å
Total Rg	24.70 Å
Atom count	3588
Residues	474
Excluded volume	63150 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yjv__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2yjv__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2yjv__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2yjv__assembly_4__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2yjv__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2yjv__assembly_6__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 (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	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	14445

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 RHLB
Molecular weight formula_weight	784.0 kDa
EC 编号 ec_number	3.6.4.12
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N

XXXXXXXXX

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	65

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2yjvA00
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	2yjvB00
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	2yjvC00
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	2yjvD00
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	2yjvE00
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	2yjvF00
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	2yjvG00
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	2yjvH00
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	2yjvI00
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	2yjvJ00
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	2yjvK00
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	2yjvL00
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

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Unit-cell length a length_a	259.630 Å
Unit-cell length b length_b	69.070 Å
Unit-cell length c length_c	123.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.17 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	122.620 Å
R factor r_factor	0.2243
R_work r_work	0.2209
R_free r_free	0.2877

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yjv__assembly_1__model_1

2yjv__assembly_1__model_1 | I(q)

2yjv__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

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

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2yjv__assembly_1__model_1

2yjv__assembly_1__model_1 | I(q)

2yjv__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) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)