SAXSdb — 9qxx

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1. Structure Basics

entry_id	9qxx
deposition_date	2025-04-16
title	JetABC DNA loaded state dimer
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	74.61 Å
rg_electron	75.57 Å
i0	5184740000.00
molecular_weight	573110.0 kDa
excluded_volume	703500 Å³
envelope_volume	1143300 Å³
shell_volume	134360 Å³
envelope_diameter	353.7 Å
shell_rg	66.23 Å
envelope_rg	76.84 Å
shape_rg	75.55 Å
total_rg	75.47 Å
total_atoms	79364
n_residues	4822
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	240.7 Å
rg_real	74.12 Å
rg_real_error	1.64 Å
i0_real	5.1620e+09
i0_real_error	1.0580e+08
rg_reciprocal	73.23 Å
i0_reciprocal	5167000000.0000
total_estimate	0.6152
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	68.8 Å
skewness	0.356
kurtosis	-0.481
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.1870
highest_alpha	298400000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.003; Oscil: 0.916; Stabil: 0.995; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.241

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	79364

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

Entity 5 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	4

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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	3.70 Å
resolution_method	—
num_particles	79015

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

JetABC DNA loaded state dimer

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 polymer

Polymer

Source

Entity 5 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)