SAXSdb — 3rfs

▼

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

Internalin B, repeat modules, Variable lymphocyte receptor B

synthetic

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D2P9A6_LISM2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–65； UniProt 36–100 Author chain B； PDBConstruct 1–65； UniProt 36–100

Internalin B, repeat modules, Variable lymphocyte receptor B

synthetic

UniProt Q4G1L3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count
2	Insufficient information	Monomer	Protein 1	MAGNESIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4G1L3_EPTBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 180–266； UniProt 146–232 Author chain B； PDBConstruct 180–266； UniProt 146–232

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	3rfs
Deposition date deposition_date	2011-04-06
Structure title title	Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering
Keywords keywords	LRR, protein binding, plasma; PROTEIN BINDING
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.

3rfs__assembly_2__model_1

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

Download this curve (.dat)

3rfs__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3rfs__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	22.32 Å
Rg (electron density)	21.43 Å
Total Rg	22.41 Å
Atom count	2061
Residues	263
Excluded volume	36934 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3rfs__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3rfs__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Internalin B, repeat modules, Variable lymphocyte receptor B
Molecular weight formula_weight	30425.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4340

ETITVSTPIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLNLAHNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPEGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIICPTHHHHHH

Source Source

Source organism organism	synthetic
Common name common_name	Inshore hagfish
NCBI taxonomy ID ncbi_taxonomy_id	32630
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	218

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3rfsA00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	3rfsB00
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

▶

Unit-cell length a length_a	31.733 Å
Unit-cell length b length_b	107.693 Å
Unit-cell length c length_c	71.277 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.06 °
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	1.700 Å
Low-resolution limit resolution_low	33.830 Å
R factor r_factor	0.1991
R_work r_work	0.1968
R_free r_free	0.2421

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

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

Internalin B, repeat modules, Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Internalin B, repeat modules, Variable lymphocyte receptor B

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

3rfs__assembly_2__model_1

3rfs__assembly_2__model_1 | I(q)

3rfs__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 (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

CATH v4.4 (2 domains)

7. Citations (1)

Design of a binding scaffold based on variable lymphocyte receptors of jawless vertebrates by module engineering

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

Internalin B, repeat modules, Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Internalin B, repeat modules, Variable lymphocyte receptor B

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

3rfs__assembly_2__model_1

3rfs__assembly_2__model_1 | I(q)

3rfs__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 (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

CATH v4.4 (2 domains)

7. Citations (1)