SAXSdb — 9qxu

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1. Structure Basics

entry_id	9qxu
deposition_date	2025-04-16
title	JetABC DNA loaded state monomer (open)
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	61.22 Å
rg_electron	61.47 Å
i0	2004100000.00
molecular_weight	342420.0 kDa
excluded_volume	416120 Å³
envelope_volume	670380 Å³
shell_volume	100290 Å³
envelope_diameter	240.1 Å
shell_rg	55.75 Å
envelope_rg	62.65 Å
shape_rg	61.39 Å
total_rg	61.55 Å
total_atoms	46869
n_residues	2791
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	221.4 Å
rg_real	62.07 Å
rg_real_error	2.57 Å
i0_real	2.0040e+09
i0_real_error	4.1370e+07
rg_reciprocal	60.49 Å
i0_reciprocal	1999000000.0000
total_estimate	0.8006
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	59.6 Å
skewness	0.737
kurtosis	0.247
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0013
highest_alpha	146000000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.626; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.531

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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	2

Polymer

type	polypeptide(L)
strand_id	C,D
atom_count	46869

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	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 4 polymer

description	JetC
formula_weight	124570.8 kDa
mutation	C61L,C336H,C401R,C568A,N721C,C753S,C942S,C1006S
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B

MNQVSGLAGKESFILTRIELFNWGGFHGLHQAAIHQDGTAVIGPTGSGKTTLVDALMTLLLANPRYNLASTGGHESDRDLISYVRGVSGPGDGGEGQSHIARPGKTVTGIAATLEREGKQVRLGALLWFDSTSSSVTDMKRLWLFSDNPGQTLEHWLNVYHEGGTRLLRQMEKEAIGLWTYPNKKQYLARLRDFFEVGENAFTLLNRAAGLKQLNSIDEIFRELVLDDHSAFDRAAEVANSFDGLTEIHQELETARKQQQSLQPVALSWEKYQKQERQLADWLTLESLLPLWFAQQASHLWREKINLLNARLAEAQTSEEQLQSQLDLQKKVVSDHMQRYLQVGGANIDELNERIKDWQKTLGSREALARQYQQLTRNLGLPSDLSQPQLEANQHEAEARREQIAVDIKLKQEEAYQKGALSHHITEELRERENERAEIARRPDSNLPAHYQAFRSELAKALNVDESELPFVAELIQVKPEEAQWRGAIERAVGSNRLRILVAPESAQEALRWVNQRNNRLHVRLLEVKLPHSPARFFDDGFTRKLLWKDHPWREAVKALLAESDRHAVDSPEQLHDTPHAMTVQGLMSGKQRFYDKHDQKRLDEDWLTGFDNRDRLNFLAKEIATLQEQVKTANAAFEFAKGEVGLLQNQAASFQKIEQIDFDSIDVPGAKSQLDALRERLENLTRPDSDASVAKAKLDEAQTIESELDKQLRAANKVTCVLDTELTLARAAERKAQQTAQQGMKEEERELSASHFPVVTLEQLPDIRDLERQHERGIQHEIERVKAELHRLNIELTKRMSEAKRVDTGALVEAGADLDDIPVYLQRLQELTEEALPEKLNRFLDYLNRSSDDGVTQLLSHIEHEVLVIEERLNELNETMFRVDFQPDRYLRLDTKKVVHESLRTLEKAQRQLNAARFVDDNGESHYKALQVLVAQLRDASERNRTLGAKALLDPRFRLEFAVSVMDRQSGNVIESRTGSQGGSGGEKEIIASYVLTASLSYALSPAGSRYPLFGTIILDEAFSRSSHAVAGRIIAALREFGLHAVFITPNKEMRLLRDHTRSAIVVHRRGQNSNMASLSWEELERHYQRRGNAG

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21

Entity 5 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 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	3.57 Å
resolution_method	—
num_particles	129606

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

JetABC DNA loaded state monomer (open)

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)