SAXSdb — 9vtr

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1. Structure Basics

entry_id	9vtr
deposition_date	2025-07-11
title	Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in full R-loop state 2
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	58.69 Å
rg_electron	58.45 Å
i0	2739320000.00
molecular_weight	417550.0 kDa
excluded_volume	511590 Å³
envelope_volume	787170 Å³
shell_volume	107480 Å³
envelope_diameter	182.5 Å
shell_rg	67.11 Å
envelope_rg	56.23 Å
shape_rg	58.49 Å
total_rg	58.47 Å
total_atoms	29332
n_residues	3595
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	182.0 Å
rg_real	58.45 Å
rg_real_error	1.50 Å
i0_real	2.7390e+09
i0_real_error	5.7450e+07
rg_reciprocal	58.86 Å
i0_reciprocal	2741000000.0000
total_estimate	0.8666
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	87.6 Å
skewness	0.041
kurtosis	-0.699
angular_range	— – 0.1350 Å⁻¹
current_alpha	0.0000
highest_alpha	217000000.0000
n_real_points	28
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.437

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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	29332

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	23304.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	2

GCTGAAGCACGTTGACGGAGCTGTTAGCATCTGCTTGAGCTTGTGGTATCTCGGACCTGACTGGGCTAATGGAAG

Entity 3 polymer

description	Non-target strand DNA
formula_weight	22949.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	3

CTTCCATTAGCCCAGTCAGGTCCGAGATACCACAAGCTCAAGCAGATGCTAACAGCTCCGTCAACGTGCTTCAGC

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	70099.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MATLAEILDNKTDDLNKDLRRAFRPLSAPVDISDTPIEALTILVNLTDRVIEQKNLLDRQKCKDKLRDEKWWANCFRTVKYRQSHNPKFPDIRANGVIRAAPVGHLPACMLSSSKLPQNSWAYANDSSQMNKSCFLTSEFIWNGDVHCLGQLLTELEHPLWNVLRKLGCYVKTAKYISKELALIPPLEINTSLVRNYLAQISLPNNEDSYISLSPVVSQSMQEDCYQVLSEHYRFSAITRFSRATNMGTLAMSCGGKFKMIRSLPPIEKYQHHHLDSVNWLTKRSVRAIRDYXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXKYLLLPNLRISGASAMNTSVSIGIPSMMAFYGFVHAFQRNVQTANPNFKIESFAVCIHNIHVENRGLTREWVPNTKGQITAPATRDDWQCDVAVSLILRCSHYSQLIPRDFIRLLPGRIARGKVTVSISDIKHLGRCLSLADAIKAIPVETGRWLSLNNEVTLNSIQDVIDELKNNKLQTVNCIGYHRLETPCEKRGSLHGYKHAFVETILGIIKFLTISENTNPSQYFWQYHYSKQGPILLPRSVSDETS

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	2.890 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.89 Å
resolution_method	—
num_particles	12291

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

Target DNA-bound type I-F3 TniQ-Cascade of Vibrio parahaemolyticus in full R-loop state 2

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)