SAXSdb — 9qcm

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1. Structure Basics

entry_id	9qcm
deposition_date	2025-03-04
last_revision	2025-09-10
title	Botulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin Complex (L-PTC)
keywords	progenitor-toxin complex, botulinum neurotoxin, hemagglutinin, TOXIN; TOXIN
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	88.77 Å
rg_electron	89.09 Å
i0	5684530000.00
molecular_weight	662790.0 kDa
excluded_volume	836970 Å³
envelope_volume	1443300 Å³
shell_volume	146620 Å³
envelope_diameter	298.1 Å
shell_rg	68.84 Å
envelope_rg	90.06 Å
shape_rg	89.12 Å
total_rg	88.67 Å
total_atoms	47012
n_residues	6207
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	230.9 Å
rg_real	85.20 Å
rg_real_error	0.71 Å
i0_real	5.4410e+09
i0_real_error	1.0250e+08
rg_reciprocal	87.06 Å
i0_reciprocal	5654000000.0000
total_estimate	0.8955
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	115.5 Å
skewness	0.130
kurtosis	-0.885
angular_range	— – 0.0900 Å⁻¹
current_alpha	1.0150
highest_alpha	217000000.0000
n_real_points	19
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.998; Stabil: 0.970; Sysdev: 1.000; Positv: 1.000; Valcen: 0.740; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Botulinum neurotoxin type B
formula_weight	152427.1 kDa
mutation	E232Q, H235Y
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	47012

MGPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHQLIYVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTEHHHHHHHHHH

Source

organism	Clostridium botulinum
ncbi_taxonomy_id	1491
host_organism	Escherichia coli

Entity 2 polymer

description	Botulinum neurotoxin type B1, nontoxic-nonhemagglutinin component, NTNH
formula_weight	138876.8 kDa
ec_number	3.4.24.69
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MNINDNLSINSPVDNKNVVVVRARKTDTVFKAFKVAPNIWVAPERYYGESLSIDEEYKVDGGIYDSNFLSQDSEKDKFLQAIITLLKRINSTNAGEKLLSLISTAIPFPYGYIGGGYYAPNMITFGSAPKSNKKLNSLISSTIPFPYAGYRETNYLSSEDNKSFYASNIVIFGPGANIVENNTVFYKKEDAENGMGTMTEIWFQPFLTYKYDEFYIDPAIELIKCLIKSLYFLYGIKPSDDLVIPYRLRSELENIEYSQLNIVDLLVSGGIDPKFINTDPYWFTDNYFSNAKKVFEDHRNIYETQIEGNNAIGNDIKLRLKQKFRININDIWELNLNYFSKEFSIMMPDRFNNALKHFYRKQYYKIDYPENYSINGFVNGQINVQLSLSDRNQDIINKPEEIINLLNGNNVSLMRSNIYGDGLKSTVDDFYSNYKIPYNRAYEYHFNNSNDSSLDNVNIGVIDNIPEIIDVNPYKENCDKFSPVQKITSTREINTNIPWPINYLQAQNTNNEKFSLSSDFVEVVSSKDKSLVYSFLSNVMFYLDSIKDNSPIDTDKKYYLWLREIFRNYSFDITATQEINTDCGINKVVTWFGKALNILNTSDSFVEEFQNLGPISLINKKENLSMPIIEIYGIPNDMLGLPLNDLNEKLFNIYLKNILYFKKVYFNFLDQWWTEYYSQYFDLICMAKQSILAQEKLIKQIIQNKLQDLFKADISMDKLNLMNLATEKTFIDLSNESQIAINNINDFLNKSAICVFDTNIYPKFISFMEQCINSVNSNVTAFIQKCTNITEDEKLQLIKLNTFMNIDFEFFDIQSIKDLITSETDLIKEEKESDYNLFLFTLQEDNNKVIEDISGKNTLVKYSDSISLVYGVNGDALYLKEPDESVSFSNKAFENGLTNSFSICFWLRNLGEDIITSKLIENKADNCGWEIYFENNGLVFSIVDCNGNEENIYLSDVISKNWYYISISIDRLRNQLLIFINDKLIANQSIEQILNIYSSNTISLVNENNPIYIEGLSILNRSITSEEVVNNYFSYLNNSYIRDISGERLEYNKTYELYNYVFPENSLYEVTENNNIYLSIKDTNNLNIQGAKFKLINIDANKQYVQKWDEGVVCLLGDEEKYVDISSENNRIQLVNSKDTAKRIIFNNDIFMPNCLTFAYNNKYLSLSLRDRNYNWMICNNNDNIPKAAHLWALKGI

Source

organism	Clostridium botulinum
ncbi_taxonomy_id	1491
host_organism	Escherichia coli

Entity 3 polymer

description	Hemagglutinin component HA70
formula_weight	71249.3 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	C,D,E

MNSSIKKIYNHIQEKVINYSDTIDLADGNYVVSRGDGWILSRQNQILGGSVISNGSTGIVGDLRVNDNAIPYYYPTPSFNEEYIKNNIQTVFANFTEANQIPIGFEFSKTAPSNKNLYMYLQYTYIRYEIIKVLQHEIIERAVLYVPSLGYVKSIEFNPGEKINKDFYFLTNDKCILNEQFLYKKILETTKNIPTNNIFNSKVSSTQRVLPYSNGLYVINKGDGYIRTNDKDLIGTLLIEAGSSGSIIQPRLRNTTRPLFTTSNDAKFSQQYTEERLKDAFNVQLFNTSTSLFKFVEEAPSNKNICIKAYNTYEKYELIDYQNGSIVNKAEYYLPSLGYCEVTNAPSPESEVVKTQVAEDGFIQNGPEEEIVVGVIDPSENIQEINTAISDNYTYNIPGIVNNNPFYILFTVNTTGIYKINAQNNLPSLKIYEAIGSGNRNFQSGNLCDDDIKAINYITGFDSPNAKSYLVVLLNKDKNYYIRVPQTSSNIENQIKFKREEGDLRNLMNSSVNIIDNLNSTGAHYYTRQSPDVHDYISYEFTIPGNFNNKDTSNIRLYTSYNQGIGTLFRVTETIDGYNLINIQQNLNLLNSTKSIRLLNGAIYILKVEVTELNNYNIKLHIDITN

Source

organism	Clostridium botulinum
ncbi_taxonomy_id	1491
host_organism	Escherichia coli

Entity 4 polymer

description	Hemagglutinin component HA17
formula_weight	16919.0 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,G,H

MSAERTFLPNGNYNIKSIFSGSLYLSPVSGSLTFSNESSANNQKWNVEYMAENRCFKISNVAEPNKYLSYDNFGFISLDSLSNRCYWFPIKIAVNTYIMLSLNKVNELDYAWDIYDTNENILSQPLLLLPNFDIYNSNQMFKLEKI

Source

organism	Clostridium botulinum
ncbi_taxonomy_id	1491
host_organism	Escherichia coli

Entity 5 polymer

description	Hemagglutinin component HA33
formula_weight	33687.6 kDa
src_method	man
entity_count	6

Polymer

type	polypeptide(L)
strand_id	I,J,K,L,M,N

MEHYSTIQNSLNDKIVTISCKANTDLFFYQVPGNGNVSLFQQTRNYLERWRIIYDSNKAAYKIKSMNIYNTNLVLTWNAPTHNISAQQDSNADNQYWLLLKDIGNNSFIIASYKNPNLVLYADTVARNLKLSTLNNSSYIKFIIEDYVISDFKNFTCRISPILAGGKVVQQVSMTNLAVNLYIWNNDLNQKWTIIYNEEKAAYQFFNKILSNGVLTWIFSDGNTVRVSSSAQNNDAQYWLINPVSDNYDRYTITNLRDKTKVLDLYGGQTADGTTIQVFNSNGGDNQIWTMSNP

Source

organism	Clostridium botulinum
ncbi_taxonomy_id	1491
host_organism	Escherichia coli

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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	2.90 Å
resolution_method	—
num_particles	139594

fit	/app/data/saxs_computation/qc/9qcm/9qcm.fit
pddf	/app/data/pr_computation/qc/9qcm/9qcm.pr.out
profile	/app/data/saxs_computation/qc/9qcm/9qcm.dat

Botulinum neurotoxin type B1, 14-subunit, Large Progenitor Toxin Complex (L-PTC)

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)