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9zbt

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

Method: ELECTRON MICROSCOPY D_max: 138.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zbt
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	39.41 Å
rg_electron	39.09 Å
i0	362605000.00
molecular_weight	137640.0 kDa
excluded_volume	165480 Å³
envelope_volume	240060 Å³
shell_volume	53645 Å³
envelope_diameter	147.4 Å
shell_rg	42.45 Å
envelope_rg	38.87 Å
shape_rg	39.05 Å
total_rg	39.41 Å
total_atoms	9594
n_residues	1098
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	138.6 Å
rg_real	39.60 Å
rg_real_error	1.66 Å
i0_real	3.6260e+08
i0_real_error	7.4240e+06
rg_reciprocal	39.48 Å
i0_reciprocal	362600000.0000
total_estimate	0.8584
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	45.0 Å
skewness	0.488
kurtosis	-0.071
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	34840000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.951; Smooth: 0.866

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Replication restart protein DnaT
formula_weight	19474.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D
atom_count	9594

MSSRVLTPDVVGIDALVHDHQTVLAKAEGGVVAVFANNAPAFYAVTPARLAELLALEEKLARPGSDVALDDQLYQEPQAAPVAVPMGKFAMYPDWQPDADFIRLAALWGVALREPVTTEELASFIAYWQAEGKVFHHVQWQQKLARSLQIGRASNGGLPKRDVNTVSEPDSQIPPGFRG

Source

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

Entity 2 polymer

description	Replication restart protein PriB
formula_weight	11459.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MTNRLVLSGTVCRAPLRKVSPSGIPHCQFVLEHRSVQEEAGFHRQAWCQMPVIVSGHENQAITHSITVGSRITVQGFISCHKAKNGLSKMVLHAEQIELIDSGD

Source

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

Entity 3 polymer

description	DNA (33-MER)
formula_weight	12206.8 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	G

GCCGCAGACTCATTTAGCCCTTATCCGTATTGCGGTCTCG

Entity 4 polymer

description	;Primosomal protein N' ;
formula_weight	81765.8 kDa
ec_number	3.6.4.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MPVAHVALPVPLPRTFDYLLPEGMTVKAGCRVRVPFGKQQERIGIVVSVSDASELPLNELKAVVEVLDSEPVFTHSVWRLLLWAADYYHHPIGDVLFHALPILLRQGRPAANAPMWYWFATEQGQAVDLNSLKRSPKQQQALAALRQGKIWRDQVATLEFNDAALQALRKKGLCDLASETPEFSDWRTNYAVSGERLRLNTEQATAVGAIHSAADTFSAWLLAGVTGSGKTEVYLSVLENVLAQGKQALVMVPEIGLTPQTIARFRERFNAPVEVLHSGLNDSERLSAWLKAKNGEAAIVIGTRSALFTPFKNLGVIVIDEEHDSSYKQQEGWRYHARDLAVYRAHSEQIPIILGSATPALETLCNVQQKKYRLLRLTRRAGNARPAIQHVLDLKGQKVQAGLAPALITRMRQHLQADNQVILFLNRRGFAPALLCHDCGWIAECPRCDHYYTLHQAQHHLRCHHCDSQRPVPRQCPSCGSTHLVPVGLGTEQLEQTLAPLFPGVPISRIDRDTTSRKGALEQQLAEVHRGGARILIGTQMLAKGHHFPDVTLVALLDVDGALFSADFRSAERFAQLYTQVAGRAGRAGKQGEVVLQTHHPEHPLLQTLLYKGYDAFAEQALAERRMMQLPPWTSHVIVRAEDHNNQHAPLFLQQLRNLILSSPLADEKLWVLGPVPALAPKRGGRWRWQILLQHPSRVRLQHIINGTLALINTIPDSRKVKWVLDVDPIEG

Source

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

Entity 5 polymer

description	DNA (33-MER)
formula_weight	12400.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

CGAGACCGCAATACGGATAAGGGCTGAGCACGCCGACGAA

Entity 6 polymer

description	DNA (11-MER)
formula_weight	4567.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	Z

TTCGTCGGCGTGCTC

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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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	3.220 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.22 Å
resolution_method	—
num_particles	857000

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

Unit Cell

Symmetry

Refinement

EM 3D

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)