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9zbu

;Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome ;

Method: ELECTRON MICROSCOPY D_max: 164.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zbu
deposition_date	2025-11-21
title	;Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome ;
keywords	DNA replication, helicase, oligomer, DNA repair, 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	46.80 Å
rg_electron	46.75 Å
i0	619220000.00
molecular_weight	188970.0 kDa
excluded_volume	230110 Å³
envelope_volume	361410 Å³
shell_volume	67548 Å³
envelope_diameter	162.5 Å
shell_rg	48.04 Å
envelope_rg	46.47 Å
shape_rg	46.72 Å
total_rg	46.91 Å
total_atoms	13223
n_residues	1563
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	164.2 Å
rg_real	47.04 Å
rg_real_error	1.90 Å
i0_real	6.1920e+08
i0_real_error	1.1780e+07
rg_reciprocal	46.80 Å
i0_reciprocal	619000000.0000
total_estimate	0.8626
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	48.3 Å
skewness	0.455
kurtosis	-0.355
angular_range	— – 0.1700 Å⁻¹
current_alpha	0.0000
highest_alpha	48500000.0000
n_real_points	35
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.896

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	DNA (36-MER)
formula_weight	10955.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	G
atom_count	13223

CCGCAGACTCATTTAGCCCTTATCCGTATTGCGGTC

Entity 2 polymer

description	DNA (33-MER)
formula_weight	10223.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

GACCGCAATACGGATAAGGGCTGAGCACGCCGA

Entity 3 polymer

description	DNA (11-MER)
formula_weight	3341.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Z

TCGGCGTGCTC

Entity 4 polymer

description	Replication restart protein PriB
formula_weight	10953.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

TNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELI

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

description	Replication restart protein DnaT
formula_weight	16851.2 kDa
src_method	man
entity_count	7

Polymer

type	polypeptide(L)
strand_id	C,D,E,T,W,X,Y

MSSRVLTPDVVGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVTPARLAELLALEEKLARPGSDVALDDQLYQEPQAAPVAVPMGKFAMYPDWQPDADFIRLAALWGVALREPVTTEELASFIAYWQAEGKVFHHVQWQQKLARSLQIGRAS

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

description	Replication restart protein PriA
formula_weight	81634.6 kDa
ec_number	5.6.2.4
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

PVAHVALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQERIGIVVSVSDASELPLNELKAVVEVLDSEPVFTHSVWRLLLWAADYYHHPIGDVLFHALPILLRQGRPAANAPMWYWFATEQGQAVDLNSLKRSPKQQQALAALRQGKIWRDQVATLEFNDAALQALRKKGLCDLASETPEFSDWRTNYAVSGERLRLNTEQATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLKGQKVQAGLAPALITRMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHHLRCHHCDSQRPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPGVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWTSHVIVRAEDHNNQHAPLFLQQLRNLILSSPLADEKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIINGTLALINTIPDSRKVKWVLDVDPIEG

Source

organism	Escherichia coli K-12
ncbi_taxonomy_id	83333
host_organism	Escherichia coli BL21(DE3)

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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resolution	3.600 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.60 Å
resolution_method	—
num_particles	212000

fit	/app/data/saxs_computation/zb/9zbu/9zbu.fit
pddf	/app/data/pr_computation/zb/9zbu/9zbu.pr.out
profile	/app/data/saxs_computation/zb/9zbu/9zbu.dat

;Visualization of PriA/PriB/DnaT complexes reveals mechanisms governing structure-specific assembly of the DNA replication restart primosome ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Refinement

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)