SAXSdb — 6frg

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

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 homooligomer	Homooligomer	Protein 2	PENTAETHYLENE GLYCOL × 4 TRIETHYLENE GLYCOL × 2 DI(HYDROXYETHYL)ETHER × 8 water × 2	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	6frg
Deposition date deposition_date	2018-02-15
Structure title title	Crystal structure of G-1F 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.

6frg__assembly_1__model_1

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

Download this curve (.dat)

6frg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6frg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.98 Å
Rg (electron density)	25.68 Å
Total Rg	26.47 Å
Atom count	5414
Residues	316
Excluded volume	47948 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6frg__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 (5)

Entity 1 Entity 1 polymer

Description description	Replicative DNA helicase
Molecular weight formula_weight	18976.9 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 Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3035

MLRESFAISGDSLISLASTGKRVPIKDLLGEKDFEIWAINEQTMKLESAKVSRVFCTGKKLVYTLKTRLGRTIKATANHRFLTIDGWKRLDELSLKEHIALPRKLESSSLQLAPEIEKLPQSDIYWDPIVSITETGVEEVFDLTVPGLRNFVANDIIVHASIEQDKLGG

Source Source

Source organism organism	Synechocystis sp. (strain PCC 6803 / Kazusa)
NCBI taxonomy ID ncbi_taxonomy_id	1111708
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	221

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6frga_
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)

CATH v4.4 (1 domains)

Domain ID domain_id	6frgA00
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	71.472 Å
Unit-cell length b length_b	71.472 Å
Unit-cell length c length_c	87.871 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 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	1.535 Å
Low-resolution limit resolution_low	43.935 Å
R factor r_factor	0.1442
R_work r_work	0.1428
R_free r_free	0.1701

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

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

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

6frg__assembly_1__model_1

6frg__assembly_1__model_1 | I(q)

6frg__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

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

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

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

6frg__assembly_1__model_1

6frg__assembly_1__model_1 | I(q)

6frg__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)