SAXSdb — 9rtj

▼

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

SF3 helicase domain-containing protein

Saccharolobus islandicus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 1	;DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3') ; × 1 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q54324_SACIS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 4–118； UniProt 256–370

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	9rtj
Deposition date deposition_date	2025-07-02
Last revision last_revision	2026-03-25
Structure title title	Hydrid structure of the helix bundle domain of pRN1 primase in complex with DNA, ATP and dGTP
Keywords keywords	primase, HBD, dinucleotide, first base-pair, REPLICATION; REPLICATION

▼

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.

9rtj__assembly_1__model_13

Assembly 1 · Model 13 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9rtj__assembly_1__model_13 | I(q)

100 plotted points; both axes use logarithmic scales.

9rtj__assembly_1__model_13 | P(r) · Pending

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

Rg（Guinier）	15.89 Å
Rg (electron density)	14.55 Å
Total Rg	15.66 Å
Atom count	2345
Residues	127
Excluded volume	21076 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rtj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`9rtj__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`9rtj__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`9rtj__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`9rtj__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`9rtj__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`9rtj__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`9rtj__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`9rtj__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`9rtj__assembly_1__model_10`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`9rtj__assembly_1__model_11`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`9rtj__assembly_1__model_12`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`9rtj__assembly_1__model_13`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`9rtj__assembly_1__model_14`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`9rtj__assembly_1__model_15`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`9rtj__assembly_1__model_16`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`9rtj__assembly_1__model_17`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`9rtj__assembly_1__model_18`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`9rtj__assembly_1__model_19`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	20	`9rtj__assembly_1__model_20`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	SF3 helicase domain-containing protein
Molecular weight formula_weight	13855.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	46900

GHMTVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRGDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVITLSKAWSVVKKYLEA

Source Source

Source organism organism	Saccharolobus islandicus
NCBI taxonomy ID ncbi_taxonomy_id	43080
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3') ;
Molecular weight formula_weight	2706.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	A

CTGTGCTCA

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Hydrid structure of the helix bundle domain of pRN1 primase in complex with DNA, ATP and dGTP

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

SF3 helicase domain-containing 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

9rtj__assembly_1__model_13

9rtj__assembly_1__model_13 | I(q)

9rtj__assembly_1__model_13 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Hydrid structure of the helix bundle domain of pRN1 primase in complex with DNA, ATP and dGTP

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

SF3 helicase domain-containing 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

9rtj__assembly_1__model_13

9rtj__assembly_1__model_13 | I(q)

9rtj__assembly_1__model_13 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)