SAXSdb — 3eus

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

DNA-binding protein

Silicibacter pomeroyi

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LU41_SILPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–86； UniProt 1–84 Author chain B； PDBConstruct 3–86； UniProt 1–84

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	3eus
Deposition date deposition_date	2008-10-10
Structure title title	The crystal structure of the DNA binding protein from Silicibacter pomeroyi
Keywords keywords	;DNA binding protein, STRUCTURAL GENOMICS, PSI2, MCSG, Protein Structure Initiative, Midwest Center for Structural Genomics, DNA-binding ;; DNA BINDING PROTEIN
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.

3eus__assembly_1__model_1

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

Download this curve (.dat)

3eus__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3eus__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.88 Å
Rg (electron density)	15.46 Å
Total Rg	16.47 Å
Atom count	1282
Residues	162
Excluded volume	22766 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3eus__assembly_1__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 (2)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3eusA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

Domain ID domain_id	3eusB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	260 — 434 Repressor (Amino-terminal Domain)
Homologous superfamily homologous superfamily	40 — lambda repressor-like DNA-binding domains

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Unit-cell length a length_a	40.164 Å
Unit-cell length b length_b	60.641 Å
Unit-cell length c length_c	68.506 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	45.410 Å
R factor r_factor	0.2035
R_work r_work	0.2010
R_free r_free	0.2537

Description description	DNA-binding protein
Molecular weight formula_weight	9699.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1376

The crystal structure of the DNA binding protein from Silicibacter pomeroyi

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

DNA-binding protein

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

3eus__assembly_1__model_1

3eus__assembly_1__model_1 | I(q)

3eus__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Silicibacter pomeroyi
NCBI taxonomy ID ncbi_taxonomy_id	89184
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	88

The crystal structure of the DNA binding protein from Silicibacter pomeroyi

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

DNA-binding protein

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

3eus__assembly_1__model_1

3eus__assembly_1__model_1 | I(q)

3eus__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)