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9qu8

apPol-DNA-nucleotide complex (ternary2)

Method: ELECTRON MICROSCOPY D_max: 104.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qu8
deposition_date	2025-04-10
last_revision	2025-10-29
title	apPol-DNA-nucleotide complex (ternary2)
keywords	DNA polymerase, REPLICATION; REPLICATION
method	ELECTRON MICROSCOPY

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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	32.23 Å
rg_electron	31.20 Å
i0	133967000.00
molecular_weight	86342.0 kDa
excluded_volume	105650 Å³
envelope_volume	142520 Å³
shell_volume	38726 Å³
envelope_diameter	106.1 Å
shell_rg	37.68 Å
envelope_rg	31.17 Å
shape_rg	31.17 Å
total_rg	31.83 Å
total_atoms	6031
n_residues	666
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	104.0 Å
rg_real	32.17 Å
rg_real_error	0.66 Å
i0_real	1.3400e+08
i0_real_error	2.0810e+06
rg_reciprocal	32.20 Å
i0_reciprocal	134000000.0000
total_estimate	0.9031
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	38.2 Å
skewness	0.240
kurtosis	-0.510
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	16500000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.929

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4. Crystallography & Experiment

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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	6031

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

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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	—

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

resolution	4.20 Å
resolution_method	—
num_particles	10241

fit	/app/data/saxs_computation/qu/9qu8/9qu8.fit
pddf	/app/data/pr_computation/qu/9qu8/9qu8.pr.out
profile	/app/data/saxs_computation/qu/9qu8/9qu8.dat

apPol-DNA-nucleotide complex (ternary2)

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)