SAXSdb — 1yvs

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

BARNASE

Bacillus amyloliquefaciens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	SULFATE ION × 6 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 12 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RNBR_BACAM
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–110； UniProt 48–157

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	1yvs
Deposition date deposition_date	1998-12-10
Structure title title	Trimeric domain swapped barnase
Keywords keywords	ENDONUCLEASE, RIBONUCLEASE, DOMAIN SWAPPED, TRIMER; ENDONUCLEASE
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.

1yvs__assembly_1__model_1

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

Download this curve (.dat)

1yvs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1yvs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.91 Å
Rg (electron density)	24.47 Å
Total Rg	25.24 Å
Atom count	2618
Residues	324
Excluded volume	45904 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1yvs__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1yvs__assembly_2__model_1`	hexameric （6）	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	BARNASE
Molecular weight formula_weight	12398.7 kDa
EC 编号 ec_number	3.1.27.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	976

AQVINTFDGVADYLQTYHKLPDNYITKSEAQALGWVASKGNLADVAPGKSIGGDIFSNREGKLPGKSGRTWREADINYTSGFRNSDRILYSSDWLIYKTTDHYQTFTKIR

Source Source

Source organism organism	Bacillus amyloliquefaciens
NCBI taxonomy ID ncbi_taxonomy_id	1390
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	102

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1yvsa_
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.1.1.2 — Bacterial ribonucleases

CATH v4.4 (1 domains)

Domain ID domain_id	1yvsA00
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	70.080 Å
Unit-cell length b length_b	70.080 Å
Unit-cell length c length_c	162.550 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	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.1870
R_work r_work	0.1870
R_free r_free	0.2440

Trimeric domain swapped barnase

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

BARNASE

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

1yvs__assembly_1__model_1

1yvs__assembly_1__model_1 | I(q)

1yvs__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Trimeric domain swapped barnase

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

BARNASE

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

1yvs__assembly_1__model_1

1yvs__assembly_1__model_1 | I(q)

1yvs__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)