SAXSdb — 2o97

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

DNA-binding protein HU-alpha

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-binding protein HU-beta × 4 （P0ACF4） NICKEL (II) ION × 4 CHLORIDE ION × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-binding protein HU-beta × 1 （P0ACF4） NICKEL (II) ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DBHA_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–90； UniProt 1–90

DNA-binding protein HU-beta

Escherichia coli

UniProt P0ACF4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	DNA-binding protein HU-alpha × 4 （P0ACF0） NICKEL (II) ION × 4 CHLORIDE ION × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA-binding protein HU-alpha × 1 （P0ACF0） NICKEL (II) ION × 1 CHLORIDE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DBHB_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–90； UniProt 1–90

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	2o97
Deposition date deposition_date	2006-12-13
Structure title title	Crystal Structure of E. coli HU heterodimer
Keywords keywords	DNA-binding, heterodimer, DNA structure, DNA supercoiling, E. coli, DNA BINDING PROTEIN; 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.

2o97__assembly_2__model_1

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

Download this curve (.dat)

2o97__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2o97__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	15.93 Å
Rg (electron density)	14.30 Å
Total Rg	15.58 Å
Atom count	1030
Residues	141
Excluded volume	18598 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2o97__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2o97__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 (5)

Entity 1 Entity 1 polymer

Description description	DNA-binding protein HU-alpha
Molecular weight formula_weight	9550.0 kDa
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	1056

MNKTQLIDVIAEKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAFVSGKALKDAVK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA-binding protein HU-beta
Molecular weight formula_weight	9239.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MNKSQLIDKIAAGADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSFRAGKALKDAVN

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	26

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2o97a_
Class class	a — All alpha proteins
Fold Fold fold	a.55 — IHF-like DNA-binding proteins
Superfamily Superfamily superfamily	a.55.1 — IHF-like DNA-binding proteins
Family Family family	a.55.1.1 — Prokaryotic DNA-bending protein

Domain ID domain_id	d2o97b1
Class class	a — All alpha proteins
Fold Fold fold	a.55 — IHF-like DNA-binding proteins
Superfamily Superfamily superfamily	a.55.1 — IHF-like DNA-binding proteins
Family Family family	a.55.1.1 — Prokaryotic DNA-bending protein

CATH v4.4 (2 domains)

Domain ID domain_id	2o97A00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	520 — HU Protein; Chain A
Homologous superfamily homologous superfamily	10 — IHF-like DNA-binding proteins

Domain ID domain_id	2o97B00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	520 — HU Protein; Chain A
Homologous superfamily homologous superfamily	10 — IHF-like DNA-binding proteins

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Unit-cell length a length_a	82.915 Å
Unit-cell length b length_b	82.915 Å
Unit-cell length c length_c	61.048 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	I 41
Space-group number int_tables_number	80
Crystal system crystal_system	—

Resolution resolution	2.450 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2280
R_work r_work	0.2260
R_free r_free	0.2640

Crystal Structure of E. coli HU heterodimer

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

DNA-binding protein HU-alpha

State in the Current Structure

Other States of the Same Protein in the Database

DNA-binding protein HU-beta

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

2o97__assembly_2__model_1

2o97__assembly_2__model_1 | I(q)

2o97__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of E. coli HU heterodimer

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

DNA-binding protein HU-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-binding protein HU-beta

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

2o97__assembly_2__model_1

2o97__assembly_2__model_1 | I(q)

2o97__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)