SAXSdb — 5t5k

▼

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

DNA-binding protein HMf-2

Methanothermus fervidus

UniProt P19267

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 6 DNA 2	DNA (90-MER) × 1 DNA (90-MER) × 1 CACODYLATE ION × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HMFB_METFE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 1–69 Author chain B； PDBConstruct 1–69； UniProt 1–69 Author chain C； PDBConstruct 1–69； UniProt 1–69 Author chain D； PDBConstruct 1–69； UniProt 1–69 Author chain E； PDBConstruct 1–69； UniProt 1–69 Author chain F； PDBConstruct 1–69； UniProt 1–69

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	5t5k
Deposition date deposition_date	2016-08-31
Structure title title	Structure of histone-based chromatin in Archaea
Keywords keywords	Nucleosome, Chromatin, Archaea Histones, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
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.

5t5k__assembly_1__model_1

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

Download this curve (.dat)

5t5k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5t5k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.12 Å
Rg (electron density)	35.57 Å
Total Rg	36.17 Å
Atom count	6831
Residues	584
Excluded volume	110420 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5t5k__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DNA-binding protein HMf-2
Molecular weight formula_weight	7683.1 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	6831

MELPIAPIGRIIKDAGAERVSDDARITLAKILEEMGRDIASEAIKLARHAGRKTIKAEDIELAVRRFKK

Source Source

Source organism organism	Methanothermus fervidus
NCBI taxonomy ID ncbi_taxonomy_id	2180
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA (90-MER)
Molecular weight formula_weight	27688.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

TATGAACCGTACTGTCGTCTGCGGCCTTTGATTATCAATTAAAGCGTTCTACGGCGTTTTTGATCGCTCAACTGTGCGAGCTAGATCTCA

Entity 3 Entity 3 polymer

Description description	DNA (90-MER)
Molecular weight formula_weight	27827.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J

TATGAGATCTAGCTCGCACAGTTGAGCGATCAAAAACGCCGTAGAACGCTTTAATTGATAATCAAAGGCCGCAGACGACAGTACGGTTCA

Entity 4 Entity 4 non-polymer

Description description	CACODYLATE ION
Molecular weight formula_weight	137.0 kDa
Source method src_method	syn
Copy count entity_count	3

▼

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	5t5kA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

Domain ID domain_id	5t5kF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	20 — Histone, subunit A
Homologous superfamily homologous superfamily	10 — Histone, subunit A

▶

Unit-cell length a length_a	99.454 Å
Unit-cell length b length_b	99.454 Å
Unit-cell length c length_c	171.730 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	36

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	4.000 Å
Low-resolution limit resolution_low	19.760 Å
R factor r_factor	0.2165
R_work r_work	0.2144
R_free r_free	0.2618

Structure of histone-based chromatin in Archaea

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

DNA-binding protein HMf-2

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

5t5k__assembly_1__model_1

5t5k__assembly_1__model_1 | I(q)

5t5k__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Structure of histone-based chromatin in Archaea

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

DNA-binding protein HMf-2

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

5t5k__assembly_1__model_1

5t5k__assembly_1__model_1 | I(q)

5t5k__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)