SAXSdb — 1jbs

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

restrictocin

OrganismNot specified

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	29-mer sarcin/ricin domain RNA analog × 1 POTASSIUM ION × 3 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	29-mer sarcin/ricin domain RNA analog × 1 POTASSIUM ION × 3 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNMG_ASPRE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–149； UniProt 28–176 Author chain B； PDBConstruct 1–149； UniProt 28–176

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	1jbs
Deposition date deposition_date	2001-06-06
Structure title title	Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog
Keywords keywords	ribotoxin, highly specific ribonuclease, protein-RNA complex, ribonuclease T1, HYDROLASE-RNA COMPLEX; HYDROLASE/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.

1jbs__assembly_2__model_1

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

Download this curve (.dat)

1jbs__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1jbs__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.68 Å
Rg (electron density)	20.05 Å
Total Rg	20.88 Å
Atom count	1823
Residues	166
Excluded volume	30120 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1jbs__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1jbs__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	29-mer sarcin/ricin domain RNA analog
Molecular weight formula_weight	9505.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	3987

CGCUCCUCAGUACGAUAGGAACCGGAGCG

Entity 2 Entity 2 polymer

Description description	restrictocin
Molecular weight formula_weight	16889.9 kDa
EC 编号 ec_number	3.1.27.-
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

ATWTCINQQLNPKTNKWEDKRLLYSQAKAESNSHHAPLSDGKTGSSYPHWFTNGYDGNGKLIKGRTPIKFGKADCDRPPKHSQNGMGKDDHYLLEFPTFPDGHDYKFDSKKPKEDPGPARVIYTYPNKVFCGIVAHQRGNQGDLRLCSH

Entity 3 Entity 3 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	341

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1jbsa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.3 — Ribotoxin

Domain ID domain_id	d1jbsb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.1 — Microbial ribonucleases
Superfamily Superfamily superfamily	d.1.1 — Microbial ribonucleases
Family Family family	d.1.1.3 — Ribotoxin

CATH v4.4 (2 domains)

Domain ID domain_id	1jbsA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

Domain ID domain_id	1jbsB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	30 — Microbial ribonucleases

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Unit-cell length a length_a	62.511 Å
Unit-cell length b length_b	101.863 Å
Unit-cell length c length_c	41.092 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.97 °
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	1.970 Å
Low-resolution limit resolution_low	19.800 Å
R factor r_factor	0.2170
R_work r_work	0.2130
R_free r_free	0.2567

Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog

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

restrictocin

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

1jbs__assembly_2__model_1

1jbs__assembly_2__model_1 | I(q)

1jbs__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of ribotoxin restrictocin and a 29-mer SRD RNA analog

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

restrictocin

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

1jbs__assembly_2__model_1

1jbs__assembly_2__model_1 | I(q)

1jbs__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)