SAXSdb — 9vtp

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1. Structure Basics

entry_id	9vtp
deposition_date	2025-07-11
title	Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in partial R-loop state
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	59.57 Å
rg_electron	59.31 Å
i0	2823880000.00
molecular_weight	424640.0 kDa
excluded_volume	520590 Å³
envelope_volume	806180 Å³
shell_volume	109080 Å³
envelope_diameter	186.2 Å
shell_rg	67.69 Å
envelope_rg	56.75 Å
shape_rg	59.34 Å
total_rg	59.37 Å
total_atoms	29818
n_residues	3647
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	186.7 Å
rg_real	59.34 Å
rg_real_error	1.54 Å
i0_real	2.8240e+09
i0_real_error	5.4300e+07
rg_reciprocal	59.73 Å
i0_reciprocal	2826000000.0000
total_estimate	0.8677
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	86.2 Å
skewness	0.047
kurtosis	-0.712
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0000
highest_alpha	168200000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.940; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.461

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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	29818

CUGAUAAUGAGAUACCACAAGCUCAAGCAGAUGCUAACAGGUGAACUGCCGAAUAGGUAG

Source

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

Entity 2 polymer

description	Target strand DNA from Vibrio alginolyticus K08M03 plasmid pL300
formula_weight	23027.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	2

CAGCCGCTTCATCATTCAGCCTGTTAGCATCTGCTTGAGCCTGTGGTATCCGGGTGTTTACGTAAGACTCTGCTT

Entity 3 polymer

description	Non-target strand DNA from Vibrio alginolyticus strain K08M3 plasmid pL300
formula_weight	23224.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	3

AAGCAGAGTCTTACGTAAACACCCGGATACCACAGGCTCAAGCAGATGCTAACAGGCTGAATGATGAAGCGGCTG

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	71108.4 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MATLAEILDNKTDDLNKDLRRAFRPLSAPVDISDTPIEALTILVNLTDRVIEQKNLLDRQKCKDKLRDEKWWANCFRTVKYRQSHNPKFPDIRANGVIRAAPVGHLPACMLSSSKLPQNSWAYANDSSQMNKSCFLTSEFIWNGDVHCLGQLLTELEHPLWNVLRKLGCYVKTAKYISKELALIPPLEINTSLVRNYLAQISLPNNEDSYISLSPVVSQSMQEDCYQVLSEHYRFSAITRFSRATNMGTLAMSCGGKFKMIRSLPPIEKYQHHHLDSVNWLTKRSVRAIRDYTESSVWVISPNKLALRKKSIIGDIKMMLSQWLRXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKYLLLPNLRISGASAMNTSVSIGIPSMMAFYGFVHAFQRNVQTANPNFKIESFAVCIHNIHVENRGLTREWVPNTKGQITAPATRDDWQCDVAVSLILRCSHYSQLIPRDFIRLLPGRIARGKVTVSISDIKHLGRCLSLADAIKAIPVETGRWLSLNNEVTLNSIQDVIDELKNNKLQTVNCIGYHRLETPCEKRGSLHGYKHAFVETILGIIKFLTISENTNPSQYFWQYHYSKQGPILLPRSVSDETS

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	2.680 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.68 Å
resolution_method	—
num_particles	31509

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

Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in partial R-loop state

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)