SAXSdb — 9qxr

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1. Structure Basics

entry_id	9qxr
deposition_date	2025-04-16
title	E. coli JetABC monomer in a DNA boarding conformation
keywords	SMC complexes, Wadjet, JetABCD, DNA loop extrusion, DNA BINDING PROTEIN; DNA BINDING 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	65.55 Å
rg_electron	65.70 Å
i0	2046710000.00
molecular_weight	346290.0 kDa
excluded_volume	420260 Å³
envelope_volume	704490 Å³
shell_volume	96735 Å³
envelope_diameter	239.2 Å
shell_rg	58.43 Å
envelope_rg	64.77 Å
shape_rg	65.65 Å
total_rg	65.69 Å
total_atoms	47325
n_residues	2828
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	214.6 Å
rg_real	66.06 Å
rg_real_error	1.89 Å
i0_real	2.0460e+09
i0_real_error	4.4310e+07
rg_reciprocal	64.98 Å
i0_reciprocal	2042000000.0000
total_estimate	0.8448
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	62.6 Å
skewness	0.444
kurtosis	-0.380
angular_range	— – 0.1200 Å⁻¹
current_alpha	0.0021
highest_alpha	127100000.0000
n_real_points	25
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.295

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	JetB
formula_weight	28020.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D
atom_count	47325

MAGFFDKLINRSVTANAGCEPEPSDEEVTDESVEDSLASSETRTLQKIREATQELLKYGLLEEASKPNLYRIVLSHPEEVTRILEPLDLDIGIDEIRGLLYVKVRLDETPAQDEWAHPLVRRQRLNLEQSLLVAILRQHFVAWEQESGTGASQAQIAIDDLLPQLQIYLGDPGSESKERTRLLTLLDQLKGHGLVTSPDAHERIVIRPIIAHLADPINLQALLAWLREQIAQQTSPNDAPEKDSSEEDVG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21

Entity 2 polymer

description	JetA
formula_weight	57818.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,J

GPAAMEENTRQRTENYISAKNQHPAWILLATRRAPLVLSCLKTLFEKSHDGIPLEEAIQSLSSILIEHVSQEQYDINQDNPFLQASRELREWIKRRLIVERDGRIFATDALEVAITFVESLDNRFMTSTASRLSTVQREIENLETRLNPNPANRVATLRRRISELERELQEAEAGHIEVLETHQAVEHIRDVYNLASSLRADFRRVEDSWREADRALRQSIIGEQYHRGDIVERLLNDQDALLNTPEGRVFDSFQQQLRQSSELKAMSERLRVILSHPSASDALNRLQRHDLRWLVKRLVDESQTVLQARARSERDVRGFMKTGLAAEHHRVGHLLNEFLNLALKLDWQRQMIRKQEVPLPAVGVAVTGIPAIERLRFKEVDDEAEQTLDLSNHAADLTQIGDDFWDAFNGLDREVLIQQTLQLLAKENRPVGLAELAELLPPAHDLETFAVWIGMAREAGIEVIDSQREFAELSDGEGRRWRFNLPTTGLESQALMDIDWEG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21

Entity 3 polymer

description	JetC
formula_weight	124562.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MNQVSGLAGKESFILTRIELFNWGGFHGLHQAAIHQDGTAVIGPTGSGKTTLVDALMTLLCANPRYNLASTGGHESDRDLISYVRGVSGPGDGGEGQSHIARPGKTVTGIAATLEREGKQVRLGALLWFDSTSSSVTDMKRLWLFSDNPGQTLEHWLNVYHEGGTRLLRQMEKEAIGLWTYPNKKQYLARLRDFFEVGENAFTLLNRAAGLKQLNSIDEIFRELVLDDHSAFDRAAEVANSFDGLTEIHQELETARKQQQSLQPVALSWEKYQKQERQLADWLTLESLLPLWFAQQASHLWREKINLLNARLAEAQTSEEQLQSQLDLQKKVVSDCMQRYLQVGGANIDELNERIKDWQKTLGSREALARQYQQLTRNLGLPSDLSQPQLEANQHEAEARCEQIAVDIKLKQEEAYQKGALSHHITEELRERENERAEIARRPDSNLPAHYQAFRSELAKALNVDESELPFVAELIQVKPEEAQWRGAIERAVGSNRLRILVAPESAQEALRWVNQRNNRLHVRLLEVKLPHSPARFFDDGFTRKLLWKDHPWREAVKALLAESDRHCVDSPEQLHDTPHAMTVQGLMSGKQRFYDKHDQKRLDEDWLTGFDNRDRLNFLAKEIATLQEQVKTANAAFEFAKGEVGLLQNQAASFQKIEQIDFDSIDVPGAKSQLDALRERLENLTRPDSDASVAKAKLDEAQTIESELDKQLRAANKVTNVLDTELTLARAAERKAQQTAQQGMKEEERELCASHFPVVTLEQLPDIRDLERQHERGIQHEIERVKAELHRLNIELTKRMSEAKRVDTGALVEAGADLDDIPVYLQRLQELTEEALPEKLNRFLDYLNRSSDDGVTQLLSHIEHEVLVIEERLNELNETMFRVDFQPDRYLRLDTKKVVHESLRTLEKAQRQLNAARFVDDNGESHYKALQVLVAQLRDACERNRTLGAKALLDPRFRLEFAVSVMDRQSGNVIESRTGSQGGSGGEKEIIASYVLTASLSYALCPAGSRYPLFGTIILDEAFSRSSHAVAGRIIAALREFGLHAVFITPNKEMRLLRDHTRSAIVVHRRGQNSNMASLSWEELERHYQRRGNAG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21

Entity 4 polymer

description	Biotinylated circular plasmid DNA (1894-MER)
formula_weight	18477.0 kDa
mutation	The DNA was modelled as polyAT track.
src_method	man
entity_count	2

Polymer

type	polydeoxyribonucleotide
strand_id	P,Q

ATATATATATATATATATATATATATATATATATATATATATATATATATATATATATAT

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 5 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	BERYLLIUM TRIFLUORIDE ION
formula_weight	66.0 kDa
src_method	syn
entity_count	2

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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	3.25 Å
resolution_method	—
num_particles	78524

fit	/app/data/saxs_computation/qx/9qxr/9qxr.fit
pddf	/app/data/pr_computation/qx/9qxr/9qxr.pr.out
profile	/app/data/saxs_computation/qx/9qxr/9qxr.dat

E. coli JetABC monomer in a DNA boarding conformation

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)