SAXSdb — 9qb8

▼

1. Structure Basics

entry_id	9qb8
deposition_date	2025-02-28
title	Lymphostatin - Conformation II - pH 8 Hepes
keywords	Virulence Factor Lymphostatin LifA Conformation II, TOXIN; TOXIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	56.94 Å
rg_electron	57.13 Å
i0	1424650000.00
molecular_weight	317170.0 kDa
excluded_volume	397670 Å³
envelope_volume	591840 Å³
shell_volume	87654 Å³
envelope_diameter	196.4 Å
shell_rg	58.00 Å
envelope_rg	56.03 Å
shape_rg	57.12 Å
total_rg	57.21 Å
total_atoms	22339
n_residues	2803
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

▼

3. P(r) Analysis (GNOM)

dmax	199.8 Å
rg_real	57.08 Å
rg_real_error	2.26 Å
i0_real	1.4250e+09
i0_real_error	3.3700e+07
rg_reciprocal	56.81 Å
i0_reciprocal	1424000000.0000
total_estimate	0.8676
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	57.1 Å
skewness	0.331
kurtosis	-0.511
angular_range	— – 0.1400 Å⁻¹
current_alpha	0.0001
highest_alpha	154600000.0000
n_real_points	29
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.810

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

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	22339

MRLPEKVLFPPVTSGLSGQEKQKKPKSITGFQENYQRNIRPIKTASEARLRFFDKMVSKENSLEDVVSLGEMIQKEIYGHEQRTFSPVHHTGNWKSSLLHNALLGLANVYNGLRETEYPNTFNRDGIKSTNSFRDNLLTKTRTPRDNFEEGIKHPEHATIPYDNDNESNKLLKAGKIAGNNNELLMEIKKESQSDHQIPLSDKFLKRKKRSPVAEDKVQNSLTPENFVQKISLSDELKTKYANEIIEIKRIMGEYNLLPDKNSRNGLKLLQKQADLLKIIMEDTSVTENTFKNIEIAITDIKREYYSHTVDIEKNIHAIWVAGSPPESISDYIKTFLKTYKEFTYYLWVDEKAFGAAKFTSVLKQIAFDLACRTIQQNTPQKNIDFINLYNEIRKKYNNNPSGQQEYLNKLRELYATYQKISTPLKHMFNSFFLENMIKLQDNFFNYCIVKGVTEINDELRINYLKNVIKLSDDDIGNYQKTINDNKDRVKKLILDLQKQFGENRISIKDVNSLTSLSKSENNHNYQTEMLLRWNYPAASDLLRMYILKEHGGIYTDTDMMPAYSKQVIFKIMMQTNGDNRFLEDLKLRRAISDGVLRYVNNQNIDEVNYNEISDADKNIIKKILTEISKMPEDSIFTKINTRIPRDTMPILRRYHLWPDGWNIRGLNGFMLSHKGSEVIDAVIAGQNQAYRELRRIRDNIHSEIYFKQTDELSSLPDTDKIGGILVKKYLSGSLFSKFRQDTIIPEALSTLQISGPDLIQRKMLQFFRSRGVLGEEFINERKLSDKAYIGVYKTTGTGKYDWLTPESIGVNDVTPADESTWCIGKGRCVDDFLFKDVSTLKTENLPELFLTKIDTDTFFSQWSTKTKKDLQKKIQDLTVRYNELIDSSTIDFKNLYEIDQMLHMIMLEMNDDIAKRSLFSLQVQISEKIRRMTIPVDNIINIYPDLHKKNDNDLSMSIKGFLASNPHTKINILYSNKTEHNIFIKDLFSFAVMENELRDIINNMSKDKTPENWEGRVMLQRYLELKMKDHLSLQSSQEANEFLEISTFIYENDFLREKIEAVKNKMNSHELYFEKIKKEQNTWQDLSTKEQKLQLIKALKEISGNTEKDSHYDRLLDAFFKKHNENIHNKIQRIKDEFKEYSRVAIHNIDKVIFKGQTLDRLYHEGYVFSDINTLSRYTLHGLGITGVHTEENLLPAPSSSLINILKEHYNEDEISAKLPLAYDYILNKKESSSIPVEILNKLSELPPHELLTPVLGQSVNPLGMGYSSDNGKITEQVIVSGADGFDNPISGLIYTYLEDLYNIHVRMREGTLNSQNLRQLLENSVSSCFLTEQSINKLLSEAEKRPYQSLTEIHQHLTGLPTIADATLSLLSVGLPGTGKLLRREQDYGRPPVTAIQDSTFVLPYNFKGIGFNDNIISSAPVASSLHFIAEHAKYTLLSWPEFYRHHAQRWFEMAKGYGSQNIDFHPQSLLVTQEGRCMGLALLYLQTEDTAHYSILQENLMTVSALHQTSNRDKLPLSKDDNSLMTRTYSLIEMLQYQGNKYITNESLLHKTAWNQERITLLFNEKGVKRALISTPNHTLVLQQLEDIYRLTDPNFGHADFLSPIDALKFIEAMIQLTPTLQEYYGLLNKDINKHIQVHYAESDMVWNKLLPENDAGLSTRIQHTTTDRLANLAEPVAVAGISLPVKTLYDIGATLDGRRITSPPTSEQIPSLRLNGDVLNDYLSRTVLTPEQADNIRKILHTQGIRSGTRPIDPEMIRGTQDDLVSSQTRLQRQATRVKQQLAGVLDTLQQHFQNIPRSSGRHLSVENIELADIGSGRFNLQIRDGETLHTTSVEVPEVVSRFQKLSTMLSALPASGIMDFDLGMSVVGVVQYARLLQQGHEDSTLAKINLAMDIKQLSEATLGSMIQIAGNKFLNTEGIQGFRLESAVAEGMRSVATRTGGTMGKALSASARVLELPVLETVLGTWNLYNSVIQLQQATSYSETMAARVQIAFDSISLGLTAASVAFPPLIIATGPIAAIGMGASSIARNVARKEERHTQWLEYKKFLTDGSKHIVVASPERGLLDFSGNKVFGKMVLDLRQSPPLLHGESSFNADRKIGHRPDLGDWQIREKVGYANSISPYSSLAHGYANSKWPRTIPKIPSGEYDTIILGYGHQYQANTEIEYLSNWIVWREAVPDSTSRHKRPPLEVLNSQCTVIAGERKTTVLPLRVLSDLTPECTEQAISLKDYKFILRGGSGGLAVQVGGAGYYDIDANLVAKENTLSFRGLPEEFPLTFDLSKQTQSVMLKTPDDEVPVMTITQKGINTLVGTAAGKDRLIGNDKDNTFHTSSGGGTVISGGGNNRYIIPRDLKTPLTLTLSSNSVSHEIFLPETTLAELKPVAFELSLIYWAGNNINVQPEDEAKLNHFAGNFRVHTRDGMTLEAVSRENGIQLAISLCDVQRWQAVYPEENNRPDAILDRLHDMGWSLTPEVRFQGGETQVSYDPLTRQLVYQLQARYSEFQLAGSRHHTTAVTGTPGSRYIIMKPVTTQILPTQIILAGDNDHPETIDLLEASPVLVEGKKDKNSVILTIATIQYSLQLTISGIEESLPETTRVAIQPQDTRLLGDVLRILPDNGNWVGIFRSGHTPTVNRLENLMALNQVMTFLPRVSGSAEQVLCLENLGGVRKKVEGELLSGKLKGAWKAEGEPTVPVNISDLSIPPYSRLYLIFEGKNNVLLRSKVHAAPLKITSAGEMQLSERQWQQQEHIIVKPDNEAPSLILSEFRRFTISSDKTFSLKLMCHQGMVRIDRRSLSVRLFYLREQPGIGSLRLTFRDFFTEVMDTTDREILEKELRPILIGDTHRFINAAYKNHLNIQLGDGVLNLADIVAEYARIQKEETSKILYQYQGAMKKKTDGPSVVEDAIMTTTVTTDSGELFPTFHPWYTDDLSGRYKSVPMARKADTLYHLTPKGDLQIIYQVATKMVNQAMIVSLPNYRHEWEKYNLSILSEIPQNNNTVVHSILRVNGPTMQVRTIDYRGTDENNPIVSFSDTTFINGEQMLSYDSHSSGRVYSREEYMMWELQQRVSEASSARTQDYWLMDAAVRNGEWKITPELLRHTPGYIRSTVSKWSRGWLKTGTILQTPEDRNTDVYLTTIQNNVFSRQGGGYQVYYRIDGMAGADIADNAPGETRCTLRPGTCFEVTSVDERHYEWNIIYVTLKTCGWSRNGQSKTPNGDNLFN

Source

organism	Escherichia coli O127:H6
ncbi_taxonomy_id	168807
host_organism	Escherichia coli

Entity 2 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	1

▶

6. Citations (1)

▶

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	3.40 Å
resolution_method	—
num_particles	298552

fit	/app/data/saxs_computation/qb/9qb8/9qb8.fit
pddf	/app/data/pr_computation/qb/9qb8/9qb8.pr.out
profile	/app/data/saxs_computation/qb/9qb8/9qb8.dat

Lymphostatin - Conformation II - pH 8 Hepes

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 (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)