SAXSdb — 2vrt

▼

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

RIBONUCLEASE E

ESCHERICHIA COLI

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	5'-R(UPUP)-3' × 1 ZINC ION × 1	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	5'-R(UPUP*GP)-3' × 1	Consistent with all polymers
3	Protein–RNA	Monomer	Protein 1 RNA 1	5'-R(UPUP*GP)-3' × 1	Consistent with all polymers
4	Protein–RNA	Monomer	Protein 1 RNA 1	5'-R(UPUP)-3' × 1 ZINC ION × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNE_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–509； UniProt 1–509 Author chain B； PDBConstruct 1–509； UniProt 1–509 Author chain C； PDBConstruct 1–509； UniProt 1–509 Author chain D； PDBConstruct 1–509； UniProt 1–509

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2vrt
Deposition date deposition_date	2008-04-14
Structure title title	Crystal Structure of E. coli RNase E possessing M1 RNA fragments - Catalytic Domain
Keywords keywords	RNA PROCESSING, M1 RNA, RNASE P, NUCLEASE, HYDROLASE, CYTOPLASM, RNA-BINDING, RNA TURNOVER, ENDONUCLEASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

2vrt__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2vrt__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vrt__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	30.61 Å
Rg (electron density)	30.55 Å
Total Rg	30.86 Å
Atom count	2979
Residues	401
Excluded volume	52425 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vrt__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vrt__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2vrt__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2vrt__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	RIBONUCLEASE E
Molecular weight formula_weight	57280.0 kDa
EC 编号 ec_number	3.1.4.-
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	13186

MKRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYGAERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRAGGISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKAAESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIKLYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEETAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQISHISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQEVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLRVRKGEETPTLSYMLPKLHEEA

Source Source

Source organism organism	ESCHERICHIA COLI
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	5'-R(UPUP)-3'
Molecular weight formula_weight	567.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E,F

UU

Entity 3 Entity 3 polymer

Description description	5'-R(UPUP*GP)-3'
Molecular weight formula_weight	912.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	G,H

UUG

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

▼

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	2vrtA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	20 — Ribonuclease E, catalytic domain

Domain ID domain_id	2vrtB04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	20 — Ribonuclease E, catalytic domain

Domain ID domain_id	2vrtC04
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	20 — Ribonuclease E, catalytic domain

Domain ID domain_id	2vrtD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1260 — Hypothetical Protein Ychn; Chain: A,
Homologous superfamily homologous superfamily	20 — Ribonuclease E, catalytic domain

▶

Unit-cell length a length_a	93.894 Å
Unit-cell length b length_b	121.252 Å
Unit-cell length c length_c	242.228 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.47 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	24.980 Å
R factor r_factor	0.3210
R_work r_work	0.3170
R_free r_free	0.3510

Crystal Structure of E. coli RNase E possessing M1 RNA fragments - Catalytic Domain

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

RIBONUCLEASE E

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

2vrt__assembly_2__model_1

2vrt__assembly_2__model_1 | I(q)

2vrt__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of E. coli RNase E possessing M1 RNA fragments - Catalytic Domain

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

RIBONUCLEASE E

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

2vrt__assembly_2__model_1

2vrt__assembly_2__model_1 | I(q)

2vrt__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)