SAXSdb — 9qxt

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1. Structure Basics

entry_id	9qxt
deposition_date	2025-04-16
title	E. coli JetABC dimer in the DNA boarding-holding state
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	81.76 Å
rg_electron	83.11 Å
i0	5266310000.00
molecular_weight	578870.0 kDa
excluded_volume	710700 Å³
envelope_volume	1257100 Å³
shell_volume	135520 Å³
envelope_diameter	305.1 Å
shell_rg	69.69 Å
envelope_rg	81.94 Å
shape_rg	83.14 Å
total_rg	82.83 Å
total_atoms	80200
n_residues	4896
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	275.3 Å
rg_real	85.91 Å
rg_real_error	1.52 Å
i0_real	5.2670e+09
i0_real_error	1.1540e+08
rg_reciprocal	79.55 Å
i0_reciprocal	5233000000.0000
total_estimate	0.8704
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	72.4 Å
skewness	0.461
kurtosis	-0.509
angular_range	— – 0.0950 Å⁻¹
current_alpha	1.8240
highest_alpha	207500000.0000
n_real_points	20
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 0.880; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.020

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	JetB
formula_weight	28004.3 kDa
mutation	C19S
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,D,H,I
atom_count	80200

MAGFFDKLINRSVTANAGSEPEPSDEEVTDESVEDSLASSETRTLQKIREATQELLKYGLLEEASKPNLYRIVLSHPEEVTRILEPLDLDIGIDEIRGLLYVKVRLDETPAQDEWAHPLVRRQRLNLEQSLLVAILRQHFVAWEQESGTGASQAQIAIDDLLPQLQIYLGDPGSESKERTRLLTLLDQLKGHGLVTSPDAHERIVIRPIIAHLADPINLQALLAWLREQIAQQTSPNDAPEKDSSEEDVG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21

Entity 2 polymer

description	JetA
formula_weight	57786.8 kDa
mutation	C36A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,J

GPAAMEENTRQRTENYISAKNQHPAWILLATRRAPLVLSALKTLFEKSHDGIPLEEAIQSLSSILIEHVSQEQYDINQDNPFLQASRELREWIKRRLIVERDGRIFATDALEVAITFVESLDNRFMTSTASRLSTVQREIENLETRLNPNPANRVATLRRRISELERELQEAEAGHIEVLETHQAVEHIRDVYNLASSLRADFRRVEDSWREADRALRQSIIGEQYHRGDIVERLLNDQDALLNTPEGRVFDSFQQQLRQSSELKAMSERLRVILSHPSASDALNRLQRHDLRWLVKRLVDESQTVLQARARSERDVRGFMKTGLAAEHHRVGHLLNEFLNLALKLDWQRQMIRKQEVPLPAVGVAVTGIPAIERLRFKEVDDEAEQTLDLSNHAADLTQIGDDFWDAFNGLDREVLIQQTLQLLAKENRPVGLAELAELLPPAHDLETFAVWIGMAREAGIEVIDSQREFAELSDGEGRRWRFNLPTTGLESQALMDIDWEG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21

Entity 3 polymer

description	JetC
formula_weight	124570.8 kDa
mutation	C61L,C336H,C401R,C568A,N721C,C753S,C942S,C1006S
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,F,G

MNQVSGLAGKESFILTRIELFNWGGFHGLHQAAIHQDGTAVIGPTGSGKTTLVDALMTLLLANPRYNLASTGGHESDRDLISYVRGVSGPGDGGEGQSHIARPGKTVTGIAATLEREGKQVRLGALLWFDSTSSSVTDMKRLWLFSDNPGQTLEHWLNVYHEGGTRLLRQMEKEAIGLWTYPNKKQYLARLRDFFEVGENAFTLLNRAAGLKQLNSIDEIFRELVLDDHSAFDRAAEVANSFDGLTEIHQELETARKQQQSLQPVALSWEKYQKQERQLADWLTLESLLPLWFAQQASHLWREKINLLNARLAEAQTSEEQLQSQLDLQKKVVSDHMQRYLQVGGANIDELNERIKDWQKTLGSREALARQYQQLTRNLGLPSDLSQPQLEANQHEAEARREQIAVDIKLKQEEAYQKGALSHHITEELRERENERAEIARRPDSNLPAHYQAFRSELAKALNVDESELPFVAELIQVKPEEAQWRGAIERAVGSNRLRILVAPESAQEALRWVNQRNNRLHVRLLEVKLPHSPARFFDDGFTRKLLWKDHPWREAVKALLAESDRHAVDSPEQLHDTPHAMTVQGLMSGKQRFYDKHDQKRLDEDWLTGFDNRDRLNFLAKEIATLQEQVKTANAAFEFAKGEVGLLQNQAASFQKIEQIDFDSIDVPGAKSQLDALRERLENLTRPDSDASVAKAKLDEAQTIESELDKQLRAANKVTCVLDTELTLARAAERKAQQTAQQGMKEEERELSASHFPVVTLEQLPDIRDLERQHERGIQHEIERVKAELHRLNIELTKRMSEAKRVDTGALVEAGADLDDIPVYLQRLQELTEEALPEKLNRFLDYLNRSSDDGVTQLLSHIEHEVLVIEERLNELNETMFRVDFQPDRYLRLDTKKVVHESLRTLEKAQRQLNAARFVDDNGESHYKALQVLVAQLRDASERNRTLGAKALLDPRFRLEFAVSVMDRQSGNVIESRTGSQGGSGGEKEIIASYVLTASLSYALSPAGSRYPLFGTIILDEAFSRSSHAVAGRIIAALREFGLHAVFITPNKEMRLLRDHTRSAIVVHRRGQNSNMASLSWEELERHYQRRGNAG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21

Entity 4 polymer

description	Circular plasmid DNA (1843-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

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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	4.13 Å
resolution_method	—
num_particles	63069

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

E. coli JetABC dimer in the DNA boarding-holding state

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)