SAXSdb — 9qbb

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1. Structure Basics

entry_id	9qbb
deposition_date	2025-03-01
title	Lymphostatin - Conformation III - pH 8
keywords	Virulence Factor Lymphostatin LifA Conformation III, 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	59.90 Å
rg_electron	60.72 Å
i0	1544730000.00
molecular_weight	330080.0 kDa
excluded_volume	413840 Å³
envelope_volume	633650 Å³
shell_volume	92251 Å³
envelope_diameter	236.6 Å
shell_rg	57.39 Å
envelope_rg	60.79 Å
shape_rg	60.75 Å
total_rg	60.56 Å
total_atoms	23257
n_residues	2911
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	217.1 Å
rg_real	60.59 Å
rg_real_error	2.54 Å
i0_real	1.5440e+09
i0_real_error	3.4460e+07
rg_reciprocal	59.31 Å
i0_reciprocal	1542000000.0000
total_estimate	0.8337
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	58.5 Å
skewness	0.681
kurtosis	0.269
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0023
highest_alpha	103500000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.712; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.707

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4. Crystallography & Experiment

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5. Entities & Polymer Info (1)

Entity 1 polymer

description	Lymphostatin
formula_weight	366421.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	23257

MRLPEKVLFPPVTSGLSGQEKQKKPKSITGFQENYQRNIRPIKTASEARLRFFDKMVSKENSLEDVVSLGEMIQKEIYGHEQRTFSPVHHTGNWKSSLLHNALLGLANVYNGLRETEYPNTFNRDGIKSTNSFRDNLLTKTRTPRDNFEEGIKHPEHATIPYDNDNESNKLLKAGKIAGNNNELLMEIKKESQSDHQIPLSDKFLKRKKRSPVAEDKVQNSLTPENFVQKISLSDELKTKYANEIIEIKRIMGEYNLLPDKNSRNGLKLLQKQADLLKIIMEDTSVTENTFKNIEIAITDIKREYYSHTVDIEKNIHAIWVAGSPPESISDYIKTFLKTYKEFTYYLWVDEKAFGAAKFTSVLKQIAFDLACRTIQQNTPQKNIDFINLYNEIRKKYNNNPSGQQEYLNKLRELYATYQKISTPLKHMFNSFFLENMIKLQDNFFNYCIVKGVTEINDELRINYLKNVIKLSDDDIGNYQKTINDNKDRVKKLILDLQKQFGENRISIKDVNSLTSLSKSENNHNYQTEMLLRWNYPAASDLLRMYILKEHGGIYTDTDMMPAYSKQVIFKIMMQTNGDNRFLEDLKLRRAISDGVLRYVNNQNIDEVNYNEISDADKNIIKKILTEISKMPEDSIFTKINTRIPRDTMPILRRYHLWPDGWNIRGLNGFMLSHKGSEVIDAVIAGQNQAYRELRRIRDNIHSEIYFKQTDELSSLPDTDKIGGILVKKYLSGSLFSKFRQDTIIPEALSTLQISGPDLIQRKMLQFFRSRGVLGEEFINERKLSDKAYIGVYKTTGTGKYDWLTPESIGVNDVTPADESTWCIGKGRCVDDFLFKDVSTLKTENLPELFLTKIDTDTFFSQWSTKTKKDLQKKIQDLTVRYNELIDSSTIDFKNLYEIDQMLHMIMLEMNDDIAKRSLFSLQVQISEKIRRMTIPVDNIINIYPDLHKKNDNDLSMSIKGFLASNPHTKINILYSNKTEHNIFIKDLFSFAVMENELRDIINNMSKDKTPENWEGRVMLQRYLELKMKDHLSLQSSQEANEFLEISTFIYENDFLREKIEAVKNKMNSHELYFEKIKKEQNTWQDLSTKEQKLQLIKALKEISGNTEKDSHYDRLLDAFFKKHNENIHNKIQRIKDEFKEYSRVAIHNIDKVIFKGQTLDRLYHEGYVFSDINTLSRYTLHGLGITGVHTEENLLPAPSSSLINILKEHYNEDEISAKLPLAYDYILNKKESSSIPVEILNKLSELPPHELLTPVLGQSVNPLGMGYSSDNGKITEQVIVSGADGFDNPISGLIYTYLEDLYNIHVRMREGTLNSQNLRQLLENSVSSCFLTEQSINKLLSEAEKRPYQSLTEIHQHLTGLPTIADATLSLLSVGLPGTGKLLRREQDYGRPPVTAIQDSTFVLPYNFKGIGFNDNIISSAPVASSLHFIAEHAKYTLLSWPEFYRHHAQRWFEMAKGYGSQNIDFHPQSLLVTQEGRCMGLALLYLQTEDTAHYSILQENLMTVSALHQTSNRDKLPLSKDDNSLMTRTYSLIEMLQYQGNKYITNESLLHKTAWNQERITLLFNEKGVKRALISTPNHTLVLQQLEDIYRLTDPNFGHADFLSPIDALKFIEAMIQLTPTLQEYYGLLNKDINKHIQVHYAESDMVWNKLLPENDAGLSTRIQHTTTDRLANLAEPVAVAGISLPVKTLYDIGATLDGRRITSPPTSEQIPSLRLNGDVLNDYLSRTVLTPEQADNIRKILHTQGIRSGTRPIDPEMIRGTQDDLVSSQTRLQRQATRVKQQLAGVLDTLQQHFQNIPRSSGRHLSVENIELADIGSGRFNLQIRDGETLHTTSVEVPEVVSRFQKLSTMLSALPASGIMDFDLGMSVVGVVQYARLLQQGHEDSTLAKINLAMDIKQLSEATLGSMIQIAGNKFLNTEGIQGFRLESAVAEGMRSVATRTGGTMGKALSASARVLELPVLETVLGTWNLYNSVIQLQQATSYSETMAARVQIAFDSISLGLTAASVAFPPLIIATGPIAAIGMGASSIARNVARKEERHTQWLEYKKFLTDGSKHIVVASPERGLLDFSGNKVFGKMVLDLRQSPPLLHGESSFNADRKIGHRPDLGDWQIREKVGYANSISPYSSLAHGYANSKWPRTIPKIPSGEYDTIILGYGHQYQANTEIEYLSNWIVWREAVPDSTSRHKRPPLEVLNSQCTVIAGERKTTVLPLRVLSDLTPECTEQAISLKDYKFILRGGSGGLAVQVGGAGYYDIDANLVAKENTLSFRGLPEEFPLTFDLSKQTQSVMLKTPDDEVPVMTITQKGINTLVGTAAGKDRLIGNDKDNTFHTSSGGGTVISGGGNNRYIIPRDLKTPLTLTLSSNSVSHEIFLPETTLAELKPVAFELSLIYWAGNNINVQPEDEAKLNHFAGNFRVHTRDGMTLEAVSRENGIQLAISLCDVQRWQAVYPEENNRPDAILDRLHDMGWSLTPEVRFQGGETQVSYDPLTRQLVYQLQARYSEFQLAGSRHHTTAVTGTPGSRYIIMKPVTTQILPTQIILAGDNDHPETIDLLEASPVLVEGKKDKNSVILTIATIQYSLQLTISGIEESLPETTRVAIQPQDTRLLGDVLRILPDNGNWVGIFRSGHTPTVNRLENLMALNQVMTFLPRVSGSAEQVLCLENLGGVRKKVEGELLSGKLKGAWKAEGEPTVPVNISDLSIPPYSRLYLIFEGKNNVLLRSKVHAAPLKITSAGEMQLSERQWQQQEHIIVKPDNEAPSLILSEFRRFTISSDKTFSLKLMCHQGMVRIDRRSLSVRLFYLREQPGIGSLRLTFRDFFTEVMDTTDREILEKELRPILIGDTHRFINAAYKNHLNIQLGDGVLNLADIVAEYARIQKEETSKILYQYQGAMKKKTDGPSVVEDAIMTTTVTTDSGELFPTFHPWYTDDLSGRYKSVPMARKADTLYHLTPKGDLQIIYQVATKMVNQAMIVSLPNYRHEWEKYNLSILSEIPQNNNTVVHSILRVNGPTMQVRTIDYRGTDENNPIVSFSDTTFINGEQMLSYDSHSSGRVYSREEYMMWELQQRVSEASSARTQDYWLMDAAVRNGEWKITPELLRHTPGYIRSTVSKWSRGWLKTGTILQTPEDRNTDVYLTTIQNNVFSRQGGGYQVYYRIDGMAGADIADNAPGETRCTLRPGTCFEVTSVDERHYEWNIIYVTLKTCGWSRNGQSKTPNGDNLFN

Source

organism	Escherichia coli O127:H6
ncbi_taxonomy_id	168807
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	3.30 Å
resolution_method	—
num_particles	219576

fit	/app/data/saxs_computation/qb/9qbb/9qbb.fit
pddf	/app/data/pr_computation/qb/9qbb/9qbb.pr.out
profile	/app/data/saxs_computation/qb/9qbb/9qbb.dat

Lymphostatin - Conformation III - pH 8

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 (1)

Entity 1 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)