SAXSdb — 9qc8

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1. Structure Basics

entry_id	9qc8
deposition_date	2025-03-04
last_revision	2025-09-10
title	BoNT-NTNH-HA70 complex from Clostridium botulinum Serotype B1
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	60.95 Å
rg_electron	60.65 Å
i0	2343170000.00
molecular_weight	419420.0 kDa
excluded_volume	528330 Å³
envelope_volume	799870 Å³
shell_volume	112310 Å³
envelope_diameter	220.8 Å
shell_rg	59.64 Å
envelope_rg	59.99 Å
shape_rg	60.70 Å
total_rg	60.43 Å
total_atoms	29799
n_residues	4107
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	216.6 Å
rg_real	61.24 Å
rg_real_error	2.37 Å
i0_real	2.3430e+09
i0_real_error	4.5600e+07
rg_reciprocal	60.68 Å
i0_reciprocal	2341000000.0000
total_estimate	0.8521
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.6 Å
skewness	0.449
kurtosis	-0.317
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0002
highest_alpha	206300000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.775; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.749

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

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	29799

MGPVTINNFNYNDPIDNNNIIMMEPPFARGTGRYYKAFKITDRIWIIPERYTFGYKPEDFNKSSGIFNRDVCEYYDPDYLNTNDKKNIFLQTMIKLFNRIKSKPLGEKLLEMIINGIPYLGDRRVPLEEFNTNIASVTVNKLISNPGEVERKKGIFANLIIFGPGPVLNENETIDIGIQNHFASREGFGGIMQMKFCPEYVSVFNNVQENKGASIFNRRGYFSDPALILMHQLIYVLHGLYGIKVDDLPIVPNEKKFFMQSTDAIQAEELYTFGGQDPSIITPSTDKSIYDKVLQNFRGIVDRLNKVLVCISDPNININIYKNKFKDKYKFVEDSEGKYSIDVESFDKLYKSLMFGFTETNIAENYKIKTRASYFSDSLPPVKIKNLLDNEIYTIEEGFNISDKDMEKEYRGQNKAINKQAYEEISKEHLAVYKIQMCKSVKAPGICIDVDNEDLFFIADKNSFSDDLSKNERIEYNTQSNYIENDFPINELILDTDLISKIELPSENTESLTDFNVDVPVYEKQPAIKKIFTDENTIFQYLYSQTFPLDIRDISLTSSFDDALLFSNKVYSFFSMDYIKTANKVVEAGLFAGWVKQIVNDFVIEANKSNTMDKIADISLIVPYIGLALNVGNETAKGNFENAFEIAGASILLEFIPELLIPVVGAFLLESYIDNKNKIIKTIDNALTKRNEKWSDMYGLIVAQWLSTVNTQFYTIKEGMYKALNYQAQALEEIIKYRYNIYSEKEKSNINIDFNDINSKLNEGINQAIDNINNFINGCSVSYLMKKMIPLAVEKLLDFDNTLKKNLLNYIDENKLYLIGSAEYEKSKVNKYLKTIMPFDLSIYTNDTILIEMFNKYNSEILNNIILNLRYKDNNLIDLSGYGAKVEVYDGVELNDKNQFKLTSSANSKIRVTQNQNIIFNSVFLDFSVSFWIRIPKYKNDGIQNYIHNEYTIINCMKNNSGWKISIRGNRIIWTLIDINGKTKSVFFEYNIREDISEYINRWFFVTITNNLNNAKIYINGKLESNTDIKDIREVIANGEIIFKLDGDIDRTQFIWMKYFSIFNTELSQSNIEERYKIQSYSEYLKDFWGNPLMYNKEYYMFNAGNKNSYIKLKKDSPVGEILTRSKYNQNSKYINYRDLYIGEKFIIRRKSNSQSINDDIVRKEDYIYLDFFNLNQEWRVYTYKYFKKEEEKLFLAPISDSDEFYNTIQIKEYDEQPTYSCQLLFKKDEESTDEIGLIGIHRFYESGIVFEEYKDYFCISKWYLKEVKRKPYNLKLGCNWQFIPKDEGWTEHHHHHHHHHH

Source

organism	Clostridium botulinum
ncbi_taxonomy_id	1491
host_organism	Escherichia coli

Entity 2 polymer

description	Non-toxic non-hemagglutinin component
formula_weight	138876.8 kDa
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

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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	465128

fit	/app/data/saxs_computation/qc/9qc8/9qc8.fit
pddf	/app/data/pr_computation/qc/9qc8/9qc8.pr.out
profile	/app/data/saxs_computation/qc/9qc8/9qc8.dat

BoNT-NTNH-HA70 complex from Clostridium botulinum Serotype B1

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 (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)