SAXSdb — 1rut

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

Fusion protein of Lmo4 protein and LIM domain-binding protein 1

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 4 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LDB1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 149–188； UniProt 300–339

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	1rut
Deposition date deposition_date	2003-12-11
Structure title title	Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain
Keywords keywords	b-tandem zipper, LIM domain, fusion protein, PROTEIN BINDING; PROTEIN BINDING
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.

1rut__assembly_1__model_1

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

Download this curve (.dat)

1rut__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rut__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.50 Å
Rg (electron density)	23.56 Å
Total Rg	23.95 Å
Atom count	1210
Residues	157
Excluded volume	21354 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rut__assembly_1__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	Fusion protein of Lmo4 protein and LIM domain-binding protein 1
Molecular weight formula_weight	20195.6 kDa
Mutation mutation	C52S, C64S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X
Atom count atom_count	1448

GSLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAANGIDDE

Source Source

Source organism organism	Mus musculus
Common name common_name	house mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	194

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1rutx1
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.3 — LIM domain

Domain ID domain_id	d1rutx2
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.3 — LIM domain

Domain ID domain_id	d1rutx3
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.3 — LIM domain

Domain ID domain_id	d1rutx4
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.3 — LIM domain

CATH v4.4 (2 domains)

Domain ID domain_id	1rutX01
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

Domain ID domain_id	1rutX02
Class class	2 — Mainly Beta
Architecture architecture	10 — Ribbon
Topology topology	110 — Cysteine Rich Protein
Homologous superfamily homologous superfamily	10 — Cysteine Rich Protein

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Unit-cell length a length_a	61.344 Å
Unit-cell length b length_b	61.344 Å
Unit-cell length c length_c	93.159 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	6

Space group space_group	P 3 1 2
Space-group number int_tables_number	149
Crystal system crystal_system	—

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	46.130 Å
R factor r_factor	0.1569
R_work r_work	0.1550
R_free r_free	0.1932

Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain

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

Fusion protein of Lmo4 protein and LIM domain-binding protein 1

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

1rut__assembly_1__model_1

1rut__assembly_1__model_1 | I(q)

1rut__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Complex of LMO4 LIM domains 1 and 2 with the ldb1 LID domain

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

Fusion protein of Lmo4 protein and LIM domain-binding protein 1

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

1rut__assembly_1__model_1

1rut__assembly_1__model_1 | I(q)

1rut__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) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

7. Citations (2)