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9rtj

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

D_max: 44.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

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

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	14.99 Å
rg_electron	14.54 Å
i0	2172190000.00
molecular_weight	351500.0 kDa
excluded_volume	421530 Å³
envelope_volume	28547 Å³
shell_volume	15320 Å³
envelope_diameter	49.0 Å
shell_rg	21.71 Å
envelope_rg	15.70 Å
shape_rg	14.49 Å
total_rg	14.77 Å
total_atoms	46900
n_residues	2540
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	44.0 Å
rg_real	14.86 Å
rg_real_error	0.21 Å
i0_real	2.1720e+09
i0_real_error	2.3000e+07
rg_reciprocal	14.87 Å
i0_reciprocal	2172000000.0000
total_estimate	0.9051
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	21.7 Å
skewness	0.006
kurtosis	-0.531
angular_range	— – 0.5000 Å⁻¹
current_alpha	0.0000
highest_alpha	568100.0000
n_real_points	80
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.974

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	SF3 helicase domain-containing protein
formula_weight	13855.1 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B
atom_count	46900

GHMTVVEFEELRKELVKRDSGKPVEKIKEEICTKSPPKLIKEIICENKTYADVNIDRSRGDWHVILYLMKHGVTDPDKILELLPRDSKAKENEKWNTQKYFVITLSKAWSVVKKYLEA

Source

organism	Saccharolobus islandicus
ncbi_taxonomy_id	43080
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	;DNA (5'-D(CPTPGPTPGPCPTPCP*A)-3') ;
formula_weight	2706.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	A

CTGTGCTCA

Entity 3 non-polymer

description	2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

fit	/app/data/saxs_computation/rt/9rtj/9rtj.fit
pddf	/app/data/pr_computation/rt/9rtj/9rtj.pr.out
profile	/app/data/saxs_computation/rt/9rtj/9rtj.dat

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

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)