SAXSdb — 9qua

▼

1. Structure Basics

entry_id	9qua
deposition_date	2025-04-10
last_revision	2025-10-29
title	apPol-DNA-nucleotide complex (ternary 1)
keywords	DNA polymerase, REPLICATION; REPLICATION
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	33.40 Å
rg_electron	32.15 Å
i0	137254000.00
molecular_weight	86962.0 kDa
excluded_volume	106240 Å³
envelope_volume	148200 Å³
shell_volume	39413 Å³
envelope_diameter	109.7 Å
shell_rg	38.05 Å
envelope_rg	32.19 Å
shape_rg	32.10 Å
total_rg	32.79 Å
total_atoms	6072
n_residues	668
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

▼

3. P(r) Analysis (GNOM)

dmax	107.8 Å
rg_real	33.38 Å
rg_real_error	0.94 Å
i0_real	1.3730e+08
i0_real_error	2.1230e+06
rg_reciprocal	33.40 Å
i0_reciprocal	137300000.0000
total_estimate	0.8989
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	39.0 Å
skewness	0.268
kurtosis	-0.481
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	14340000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.876

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Plastid replication-repair enzyme
formula_weight	76473.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6072

MGSSHHHHHHSQDPENLYFQGDEITKKYIKDNIINVDDNIIKKKDIFKLKNENNEITECAFEYFESKKKFDDDIESRFFIINDNNYNENINLIYKDIKYCGLNIQTTGLEVFDENIRLIQIAVENYPVIIYDMFNINKKDILDGLRKVLENKNIIKIIQNGKFDAKFLLHNNFKIENIFDTYIASKLLDKNKNMYGFKLNNIVEKYLNVILDKQQQNSVWNNSLLNNNQLFYAARDSSCLLKLYKKLKEEIKKENLHIVNDIENKCILPICDMELNGIKVDLENLQKSTNEILNELNIEKDNLKKKLKDENINVNSQQQVLKALQKNNVRDISNKLIENTSDSNLKNFLNHEEIISLRNYRRLYKLYSAFYLKLPLHINTKTNKIHTTFNQLKTFSGRFSSEKPNLQQIPRQKNIREIFIPNDNNIFIIADFKQIELKIAAEITNDEIMLKAYNNNIDLHTLTASIITKKNIPDINKEDRHIAKAINFGLIYGMNYVNLKNYANTYYGLNMSLDQCLYFYNSFFEHYKGIYKWHNQVKQKRALQYSTLSNRKVIFPYFSFTKALNYPVQGTCADILKLALVDLYDNLKDINGKIILCVHDEIIIEVNKKFQEEALKILVQSMENSASYFLKKVKCEVSVKIAENWGSKD

Source

organism	Plasmodium falciparum
common_name	malaria parasite P. falciparum
ncbi_taxonomy_id	5833
host_organism	Escherichia coli

Entity 2 polymer

description	DNA primer strand
formula_weight	7715.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

CAGGTGTCAGTCAGCTAGTGCTGAC

Entity 3 polymer

description	DNA template strand
formula_weight	11023.1 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

GCTACCGTAGCGTCAGCACTAGCTGACTGACACCTG

Entity 4 non-polymer

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

▶

6. Citations (1)

▶

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	—

resolution	4.200 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	4.20 Å
resolution_method	—
num_particles	9780

fit	/app/data/saxs_computation/qu/9qua/9qua.fit
pddf	/app/data/pr_computation/qu/9qua/9qua.pr.out
profile	/app/data/saxs_computation/qu/9qua/9qua.dat

apPol-DNA-nucleotide complex (ternary 1)

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

Refinement

EM 3D

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)