SAXSdb — 9ydo

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1. Structure Basics

entry_id	9ydo
deposition_date	2025-09-22
title	LPHT-ring in Vibrio cholerae at assembled, opened state
keywords	In situ cryo-EM, sheathed flagellar motor, Vibrio cholerae, LP-ring, assembled state, MOTOR PROTEIN; MOTOR 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	— Å
rg_electron	120.70 Å
i0	157265000000.00
molecular_weight	3356900.0 kDa
excluded_volume	4185200 Å³
envelope_volume	7728300 Å³
shell_volume	491430 Å³
envelope_diameter	346.5 Å
shell_rg	141.80 Å
envelope_rg	115.50 Å
shape_rg	120.80 Å
total_rg	120.60 Å
total_atoms	236015
n_residues	30589
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	346.7 Å
rg_real	121.70 Å
rg_real_error	1.17 Å
i0_real	1.5350e+11
i0_real_error	3.3530e+09
rg_reciprocal	123.40 Å
i0_reciprocal	157900000000.0000
total_estimate	0.9001
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	186.7 Å
skewness	-0.010
kurtosis	-0.807
angular_range	— – 0.0650 Å⁻¹
current_alpha	1.8610
highest_alpha	18440000000.0000
n_real_points	14
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.989; Stabil: 0.917; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Flagellar L-ring protein
formula_weight	24256.5 kDa
src_method	nat
entity_count	26

Polymer

type	polypeptide(L)
strand_id	Aa,Ab,Ac,Ad,Ae,Af,Ag,Ah,Ai,Aj,Ak,Al,Am,An,Ao,Ap,Aq,Ar,As,At,Au,Av,Aw,Ax,Ay,Az
atom_count	236015

TTTVDAVEGDKSESNSGLTDALRNRTDPVAGDPAWAPIHPKGKPEHYAAETGSLFNLASSSSMYDDSKPRGVGDIITVTLNESTKAAKSADADLNKKNDASMDPLAVGGKDLTIGDYNFSYALKNDNKFSGSAAANQSNSMSGSITVEVIEVLANGNLVIRGEKWLTLNTGDEYIRLSGTIRPDDIDFDNTIASNRISNARIQYSGTGTNQDMQEPGFLARFFNVSL

Entity 2 polymer

description	Flagellar P-ring protein
formula_weight	35702.6 kDa
src_method	nat
entity_count	26

Polymer

type	polypeptide(L)
strand_id	Ba,Bb,Bc,Bd,Be,Bf,Bg,Bh,Bi,Bj,Bk,Bl,Bm,Bn,Bo,Bp,Bq,Br,Bs,Bt,Bu,Bv,Bw,Bx,By,Bz

ARIKDVAQVAGVRNNQLVGYGLVTGLPGTGESTPFTDQSFNAMLQSFGIQLPPGTKPKTKNVAAVIVTADLPAFSKQGQTIDITVSSIGSAKSLRGGTLMQTFLKGLDGQVYAVAQGNLVVSGFSATGADGSKIVGNNPTVGMISSGAIVEREVPNPFGRGDYITFNLFESDFTTAQRLADAVNQFLGPQMASAVDAASIKVRAPRDLSQRVAFLSAIENLEFNPADSAAKIIVNSRTGTIVVGQNVRLKPAAVTHGGMTVAIKENLNVSQPNALGGGQTVVVPNTEIEVTEKQGKMFKLEPGVTLDDLVRAVNEVGAAPSDLMAILQALKQAGAIEGQLIII

Entity 3 polymer

description	Flagellar protein FlgT
formula_weight	39808.2 kDa
src_method	nat
entity_count	26

Polymer

type	polypeptide(L)
strand_id	Ca,Cb,Cc,Cd,Ce,Cf,Cg,Ch,Ci,Cj,Ck,Cl,Cm,Cn,Co,Cp,Cq,Cr,Cs,Ct,Cu,Cv,Cw,Cx,Cy,Cz

YEVTGSAAIVSSEEVARLHALEDALYKAVNFAGADIGSISNLMPLLESDRREYLFANHEVRYILIEERKAINNVMYVRTRIDIYPSATACHVEQYKKTMLIGNIDLASPQQAVMGQIYQVGDDFAQVINRRLEQESRSFVSVGTTQYDIDPKAPERIKMIAQDAGAQYIMGGMITDLTATIEQKTLQDDIINRQFAMEISVFDGKTGNEVMTRTYREVARWPFPKTSQIDTRSARFWASTYGEMMLRVSRNIMLDLESEISCKITLPQIVAKFGTTATMDLGRIHGVKQGDKLSLWHTGAFIDQQGLPRNKVTQSEITLTVSRVYEHEAELTVDQPELAYSIQIGDVMHKQM

Entity 4 polymer

description	Sodium-type flagellar protein MotY
formula_weight	31307.1 kDa
src_method	nat
entity_count	26

Polymer

type	polypeptide(L)
strand_id	Da,Db,Dc,Dd,De,Df,Dg,Dh,Di,Dj,Dk,Dl,Dm,Dn,Do,Dp,Dq,Dr,Ds,Dt,Du,Dv,Dw,Dx,Dy,Dz

LEVRYMATPQQSTWQMATNTPLECRLVHPIPNYGDAEFSSRAGKKINLDFELKMRRPMGDTRNVSLVSMPPVWRPGEGADRITNLQFFKQFDGYIGGQTAWSLLSELEKGRYPTFSYQDWQSRDQRIEVALSSVLFQQPYNEFSDCISKLLPYSFEDISFTILHYDQGTSVELNKASQKRLAQIAEYVRYNQDIDLVLVSTYTDSTDTNNNSQNLSEQRAEVLREYFKSIGLPEDRIQVQGYGKRRPIADNASPIGKDKNRRVVISLGRTQV

Entity 5 polymer

description	Flagellar assembly lipoprotein FlgP
formula_weight	1792.1 kDa
src_method	nat
entity_count	52

Polymer

type	polypeptide(L)
strand_id	;Fa,Fb,Fc,Fd,Fe,Ff,Fg,Fh,Fi,Fj,Fk,Fl,Fm,Fn,Fo,Fp,Fq,Fr,Fs,Ft,Fu,Fv,Fw,Fx,Fy,Fz,Ga,Gb,Gc,Gd,Ge,Gf,Gg,Gh,Gi,Gj,Gk,Gl,Gm,Gn,Go,Gp,Gq,Gr,Gs,Gt,Gu,Gv,Gw,Gx,Gy,Gz ;

GEVQQVPEKRQMTLF

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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	triclinic

resolution	2.69 Å
resolution_method	—
num_particles	112879

fit	/app/data/saxs_computation/yd/9ydo/9ydo.fit
pddf	/app/data/pr_computation/yd/9ydo/9ydo.pr.out
profile	/app/data/saxs_computation/yd/9ydo/9ydo.dat

LPHT-ring in Vibrio cholerae at assembled, opened 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

EM 3D

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)