SAXSdb — 9vtq

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1. Structure Basics

entry_id	9vtq
deposition_date	2025-07-11
title	Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in full R-loop state 1
keywords	CRISPR-associated transposon, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	60.82 Å
rg_electron	60.63 Å
i0	2811650000.00
molecular_weight	426210.0 kDa
excluded_volume	523560 Å³
envelope_volume	815400 Å³
shell_volume	108160 Å³
envelope_diameter	189.4 Å
shell_rg	68.43 Å
envelope_rg	58.21 Å
shape_rg	60.66 Å
total_rg	60.66 Å
total_atoms	29928
n_residues	3619
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	193.3 Å
rg_real	60.63 Å
rg_real_error	2.33 Å
i0_real	2.8120e+09
i0_real_error	6.0060e+07
rg_reciprocal	60.94 Å
i0_reciprocal	2813000000.0000
total_estimate	0.8682
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	89.2 Å
skewness	0.082
kurtosis	-0.703
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	179200000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.477

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	crRNA from Vibrio parahaemolyticus
formula_weight	19405.7 kDa
src_method	man
entity_count	1

Polymer

type	polyribonucleotide
strand_id	1
atom_count	29928

CUGAUAAUGAGAUACCACAAGCUCAAGCAGAUGCUAACAGGUGAACUGCCGAAUAGGUAG

Source

organism	Vibrio parahaemolyticus RIMD 2210633
ncbi_taxonomy_id	223926
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Target strand DNA
formula_weight	30950.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	2

CTAATGGAAGTGCCTCTGTCGCAGTGATGTGCCTAGCTGAAGCACGTTGACGGAGCTGTTAGCATCTGCTTGAGCTTGTGGTATCTCGGACCTGACTGAC

Entity 3 polymer

description	Non-target strand DNA
formula_weight	30751.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	3

GTCAGTCAGGTCCGAGATACCACAAGCTCAAGCAGATGCTAACAGCTCCGTCAACGTGCTTCAGCTAGGCACATCACTGCGACAGAGGCACTTCCATTAG

Entity 4 polymer

description	Type I-F CRISPR-associated protein Csy3
formula_weight	39455.4 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F

MKLPNGLSYMKSIEASDVIFLVNWPDGRKTPLPYTSRVALGMKEGSKSAYKYDGQIDADVTAYSLAQGNPHEIDFCCVPYGAESIECEFSVSFASSLRKPFKCSDPEVKRTLVQLIKLYEEKVGWEELANRFLENICNGRWLWRNNECTYSTSIGIKPWPWEDEKAISPFHDIRKNYAGTNHFRDHKDWDNLIKLITDAFSQPNGLCIFEVSATFRLGTNAPIYPSQVFKDSVKGEKNRIYQSTDVDGESSPILGCYKTGAAIATIDDWYPDADKPIRISHYGAHREDVYCYRHPNTGKDLFTLLEKADQYLEQLQATDVLPDEMINDLHFIVANLIKGGLLQQKGT

Source

organism	Vibrio parahaemolyticus RIMD 2210633
ncbi_taxonomy_id	223926
host_organism	Escherichia coli BL21(DE3)

Entity 5 polymer

description	CRISPR-associated protein Csy2
formula_weight	73021.9 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MATLAEILDNKTDDLNKDLRRAFRPLSAPVDISDTPIEALTILVNLTDRVIEQKNLLDRQKCKDKLRDEKWWANCFRTVKYRQSHNPKFPDIRANGVIRAAPVGHLPACMLSSSKLPQNSWAYANDSSQMNKSCFLTSEFIWNGDVHCLGQLLTELEHPLWNVLRKLGCYVKTAKYISKELALIPPLEINTSLVRNYLAQISLPNNEDSYISLSPVVSQSMQEDCYQVLSEHYRFSAITRFSRATNMGTLAMSCGGKFKMIRSLPPIEKYQHHHLDSVNWLTKRSVRAIRDYTESSVWVISPNKLALRKKSIIGDIKMMLSQWLRTTPTHEEKLDIRKLTERFNVDLAKTKFANRYAYDPLLTQLIYNCIGSIIHSPPQYAPKCEGNDDKYLLLPNLRISGASAMNTSVSIGIPSMMAFYGFVHAFQRNVQTANPNFKIESFAVCIHNIHVENRGLTREWVPNTKGQITAPATRDDWQCDVAVSLILRCSHYSQLIPRDFIRLLPGRIARGKVTVSISDIKHLGRCLSLADAIKAIPVETGRWLSLNNEVTLNSIQDVIDELKNNKLQTVNCIGYHRLETPCEKRGSLHGYKHAFVETILGIIKFLTISENTNPSQYFWQYHYSKQGPILLPRSVSDETS

Source

organism	Vibrio parahaemolyticus RIMD 2210633
ncbi_taxonomy_id	223926
host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

description	CRISPR-associated protein, Csy4 family
formula_weight	22919.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MDWHYRTITFLPEYRNNEAIAAKCIKELHRFNYKYETRSIGVSFPLWGQETVGRKITFVSTNKMELDFLISRRYFVQMTKLGYFSISTTQTVPDDCSYVLFKRAHSIDKGTFAGRARELKRLERRALERGEIFDPIAYSKTTSHAFQSYHSLEEDSSSGNKFRLNIQMKERSGTVGTGKFSSYGLGNTDNSLQVVPLI

Source

organism	Vibrio parahaemolyticus RIMD 2210633
ncbi_taxonomy_id	223926
host_organism	Escherichia coli BL21(DE3)

Entity 7 polymer

description	TniQ
formula_weight	47357.1 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	I,J

GPRISEFMVQMMLLQRPKSYPDESLESFFIRVANKNGYNDVHWFLVAVKRYLLDIDPRKFQTFPTDICCINPYSSKKHSISRTHALHHLSQLTFNEPVDLLGIALNRNQMQFSPSTTALIRGAEVIPRSLLRKGAIPCCPCCLGEHGYASYRWHFSGYEYCHEHDVKLIERCSCGAIYDYRYAGLSGVCTECGENISASQENHEPKATRIASWLAGDDVKPLPDVPLSYRWGFMHWWSQISSSCKTRNNGEFLAFWEHWPNSFHKLIGKEIDFNFEYCVLSKNDLRVKDILGKILFSSIQLPDRNFRSNIILKEMFQYIETHLWDDNGKLANLRMNMLEICVLLNCSREQVTSMIEQGLLPPNRQLGKREILIVTEYAFYLGDVYCLWLSEFQSDEFNRSFYLSRW

Source

organism	Vibrio parahaemolyticus RIMD 2210633
ncbi_taxonomy_id	223926
host_organism	Escherichia coli BL21(DE3)

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 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	2.840 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.84 Å
resolution_method	—
num_particles	36247

fit	/app/data/saxs_computation/vt/9vtq/9vtq.fit
pddf	/app/data/pr_computation/vt/9vtq/9vtq.pr.out
profile	/app/data/saxs_computation/vt/9vtq/9vtq.dat

Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in full R-loop state 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 (8)

Entity 1 polymer

Polymer

Source

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 polymer

Polymer

Source

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)