SAXSdb — 9yfg

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1. Structure Basics

entry_id	9yfg
deposition_date	2025-09-25
title	Flagellar outer membrane complex in Vibrio cholerae at disassembled, closed state
keywords	Vibrio cholerae, in situ cryo-EM, closed, flagellar outer membrane complex, 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	152.40 Å
i0	487519000000.00
molecular_weight	5869400.0 kDa
excluded_volume	7299400 Å³
envelope_volume	12915000 Å³
shell_volume	670530 Å³
envelope_diameter	453.9 Å
shell_rg	150.40 Å
envelope_rg	147.80 Å
shape_rg	152.40 Å
total_rg	152.30 Å
total_atoms	412635
n_residues	52997
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	491.3 Å
rg_real	155.10 Å
rg_real_error	3.14 Å
i0_real	4.8010e+11
i0_real_error	1.2370e+10
rg_reciprocal	143.60 Å
i0_reciprocal	460500000000.0000
total_estimate	0.8897
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	147.4 Å
skewness	0.201
kurtosis	-0.661
angular_range	— – 0.0500 Å⁻¹
current_alpha	1.5900
highest_alpha	19010000000.0000
n_real_points	11
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.972; Stabil: 0.906; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Flagellar L-ring protein
formula_weight	24256.5 kDa
src_method	man
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	412635

TTTVDAVEGDKSESNSGLTDALRNRTDPVAGDPAWAPIHPKGKPEHYAAETGSLFNLASSSSMYDDSKPRGVGDIITVTLNESTKAAKSADADLNKKNDASMDPLAVGGKDLTIGDYNFSYALKNDNKFSGSAAANQSNSMSGSITVEVIEVLANGNLVIRGEKWLTLNTGDEYIRLSGTIRPDDIDFDNTIASNRISNARIQYSGTGTNQDMQEPGFLARFFNVSL

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

Entity 2 polymer

description	Flagellar P-ring protein
formula_weight	35702.6 kDa
src_method	man
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

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

Entity 3 polymer

description	Flagellar protein FlgT
formula_weight	39808.2 kDa
src_method	man
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

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

Entity 4 polymer

description	Sodium-type flagellar protein MotY
formula_weight	31208.0 kDa
src_method	man
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

LEVRYMATPQQSTWQMATNTPLECRLVHPIPNYGDAEFSSRAGKKINLDFELKMRRPMGDTRNVSLVSMPPVWRPGEGADRITNLQFFKQFDGYIGGQTAWSLLSELEKGRYPTFSYQDWQSRDQRIEVALSSVLFQQPYNEFSDCISKLLPYSFEDISFTILHYDQGTSVELNKASQKRLAQIAEYVRYNQDIDLVLVSTYTDSTDTNNNSQNLSEQRAEVLREYFKSIGLPEDRIQVQGYGKRRPIADNASPIGKDKNRRVVISLGRTQ

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

Entity 5 polymer

description	Sodium-type flagellar protein MotX
formula_weight	21244.1 kDa
src_method	man
entity_count	26

Polymer

type	polypeptide(L)
strand_id	Ea,Eb,Ec,Ed,Ee,Ef,Eg,Eh,Ei,Ej,Ek,El,Em,En,Eo,Ep,Eq,Er,Es,Et,Eu,Ev,Ew,Ex,Ey,Ez

PVPIYSEAELIKLIEENKHLERVKADNCQIVEDIVARATRISLPSYEFLYGDMLAWGVCVDQDVELGLYYMENAAHQGLPAALEQLGRYYSRGTLVQQDKERAIPYLREAAAMGNLNARIQLAELLLRDYGSPLDYEDAYRWLYNSVTADQRTHNRIALLRQGLERRMPENIIARAKRRETFW

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

Entity 6 polymer

description	FlgP
formula_weight	1506.8 kDa
src_method	man
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 ;

QQVPEKRQMTLF

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

Entity 7 polymer

description	Lipoprotein
formula_weight	11947.4 kDa
src_method	man
entity_count	58

Polymer

type	polypeptide(L)
strand_id	;Ha,Hc,He,Hg,Hi,Hk,Hm,Ho,Hq,Hs,Hu,Hw,Hy,Ia,Ic,Ie,Ig,Ii,Ik,Im,Io,Iq,Is,Iu,Iw,Iy,Ja,Jc,Je,Jg,Ji,Jk,Jm,Jo,Jq,Js,Ju,Jw,Jy,Ka,Kc,Ke,Kg,Ki,Kk,Km,Ko,Kq,Ks,Ku,Kw,Ky,La,Lc,Le,Lg,Li,Lk ;

PDDWLTAVGYANISEQRGRDEAEKQVRAMRASKIDAYRELAEQVYGMRISGRAELQDQRLGTELTAGAVDGVIRGAEVVRSYKVGDSYVTELRLDIRKMDKMRDY

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

Entity 8 polymer

description	FlgO domain-containing protein
formula_weight	21395.1 kDa
src_method	man
entity_count	58

Polymer

type	polypeptide(L)
strand_id	;Hb,Hd,Hf,Hh,Hj,Hl,Hn,Hp,Hr,Ht,Hv,Hx,Hz,Ib,Id,If,Ih,Ij,Il,In,Ip,Ir,It,Iv,Ix,Iz,Jb,Jd,Jf,Jh,Jj,Jl,Jn,Jp,Jr,Jt,Jv,Jx,Jz,Kb,Kd,Kf,Kh,Kj,Kl,Kn,Kp,Kr,Kt,Kv,Kx,Kz,Lb,Ld,Lf,Lh,Lj,Ll ;

IYNGKEPYNGSQFMLMESPRHTLDFFVESMTEDLMLSNTSITARTPIAVTSFVDLQNMDTTNWLGNSVSEGFIHQFQRRGFKVVDFKTTGSIQVTQQGDFAFSRDWKNLSSEQEVQYVLTGTMLRQEGGVIVNARVVGMHSRIVVATAQGFLPADRIGRDLDTLNSIRTQDGVLIRSDPTITQPYTVILR

Source

organism	Vibrio cholerae O1 biovar El Tor str. N16961
ncbi_taxonomy_id	243277
host_organism	Vibrio cholerae O1 biovar El Tor str. N16961

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6. Citations (1)

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resolution	3.55 Å
resolution_method	—
num_particles	177296

fit	/app/data/saxs_computation/yf/9yfg/9yfg.fit
pddf	/app/data/pr_computation/yf/9yfg/9yfg.pr.out
profile	/app/data/saxs_computation/yf/9yfg/9yfg.dat

Flagellar outer membrane complex in Vibrio cholerae at disassembled, closed state

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Source

Entity 7 polymer

Polymer

Source

Entity 8 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)