SAXSdb — 6fre

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

Replicative DNA helicase,Replicative DNA helicase

Synechocystis sp. (strain PCC 6803 / Kazusa)

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNAB_SYNY3
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–112； UniProt 376–486 Author chain A； PDBConstruct 118–165； UniProt 767–814

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	6fre
Deposition date deposition_date	2018-02-15
Structure title title	Crystal structure of G-1F/H73A mutant of Ssp DnaB Mini-Intein variant M86
Keywords keywords	intein, protein splicing, Hint domain fold, pre-splicing form, SPLICING; SPLICING
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.

6fre__assembly_1__model_1

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

Download this curve (.dat)

6fre__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6fre__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.90 Å
Rg (electron density)	14.62 Å
Total Rg	15.97 Å
Atom count	2415
Residues	154
Excluded volume	21564 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6fre__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 (2)

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6frea1
Class class	b — All beta proteins
Fold Fold fold	b.86 — Hedgehog/intein (Hint) domain
Superfamily Superfamily superfamily	b.86.1 — Hedgehog/intein (Hint) domain
Family Family family	b.86.1.2 — Intein (protein splicing domain)

Domain ID domain_id	d6frea2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	6freA00
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	16 — Endonuclease - Pi-scei; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — Hedgehog/Intein (Hint) domain

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Unit-cell length a length_a	52.583 Å
Unit-cell length b length_b	52.583 Å
Unit-cell length c length_c	118.338 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 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	1.220 Å
Low-resolution limit resolution_low	48.050 Å
R factor r_factor	0.1757
R_work r_work	0.1750
R_free r_free	0.1884

Description description	Replicative DNA helicase,Replicative DNA helicase
Molecular weight formula_weight	18909.8 kDa
EC 编号 ec_number	3.6.4.12,3.6.4.12
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2966

Crystal structure of G-1F/H73A mutant of Ssp DnaB Mini-Intein variant M86

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

Replicative DNA helicase,Replicative DNA helicase

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

6fre__assembly_1__model_1

6fre__assembly_1__model_1 | I(q)

6fre__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
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	247

Crystal structure of G-1F/H73A mutant of Ssp DnaB Mini-Intein variant M86

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

Replicative DNA helicase,Replicative DNA helicase

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

6fre__assembly_1__model_1

6fre__assembly_1__model_1 | I(q)

6fre__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)