SAXSdb — 9qcc

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1. Structure Basics

entry_id	9qcc
deposition_date	2025-03-04
title	Activated XauSPARDA filament assembly with bound dsDNA substrate
keywords	short prokaryotic Argonaute, bacterial defence system, DREN domain, DREN-APAZ, RNA BINDING PROTEIN; RNA 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	74.06 Å
rg_electron	74.12 Å
i0	11797400000.00
molecular_weight	856490.0 kDa
excluded_volume	1045600 Å³
envelope_volume	1551600 Å³
shell_volume	178230 Å³
envelope_diameter	271.0 Å
shell_rg	70.49 Å
envelope_rg	73.11 Å
shape_rg	74.12 Å
total_rg	74.05 Å
total_atoms	60098
n_residues	7022
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	223.9 Å
rg_real	73.60 Å
rg_real_error	1.10 Å
i0_real	1.1740e+10
i0_real_error	2.0500e+08
rg_reciprocal	73.10 Å
i0_reciprocal	11770000000.0000
total_estimate	0.8419
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	74.7 Å
skewness	0.479
kurtosis	-0.218
angular_range	— – 0.1050 Å⁻¹
current_alpha	0.0479
highest_alpha	393100000.0000
n_real_points	22
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.934; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.147

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	DUF4365 domain-containing protein
formula_weight	52420.3 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,E,I,M,Q,U,W,Y
atom_count	60115

MGGSHHHHHHGMASMSKRITDSQVLGELGETAIKKIVLETGFLYEQRGRLEAGTDGIIELRDPKSGAPLGKLLGVQVKSTESGQYVRENDNSFEYLLKPDDLKYWRTSNIPVIIVLWRKSDETAYWKDVSDCVRGEERRLKFDKGTDVFDPRSADRIGALTIDRRTPGVFLPPLNKGEDAIINLLRIRLPDEIFISTSPFGSGRDAVPELVKHGNVRFDWVIRKRRFVSFFDPREYGTRAIVDLDQVEAVDTKLIAFNDEQDDLNDTMDLLRRTVERQTATQLSFLRKDRLFHFKAVGVGKSRSYRYMSNVNETSAKVVSAYSSKKKDGWGYVRHHAARLRFERLADEWFLVIDPDFHFTTDGFQPHRYPEALLAGKKRLERNAAVRGQVTMWQHLLVESGKHEVGLFDADKPAPLLQFERLPVIQLSQAVPESSWNRTDPRAKEMEAQDLFEEGGVG

Source

organism	Xanthobacter autotrophicus Py2
ncbi_taxonomy_id	78245
host_organism	Escherichia coli

Entity 2 polymer

description	Protein argonaute
formula_weight	53589.7 kDa
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	B,F,J,N,R,V,X,Z

MTFKAHVFDEPMLEFGDGGQHCDPRQGLREHGPLQPRSGDVIRVGVIGTDDTVAGFTEFLAETGRGIESGNKQLINLNPDFPGLGNQNPFRCKFEVPDGATVTISRRQVNDITGIGRHDEAVRHAVELISSQLSALVEGSAKPDVIVLALPIPLIEKLVNAKSEGEDSDDDVDGGDMLNFRDLLKAKTLHLPVPTQIVWPDTWDDAAKIPRKIKRDSNRQTQVKATRAWNLLNALFYKAGKVPWRLLPDQAEYRTSFLGIGFYRDLDGQQLWTSTAQMFDERGRGLILRGARAQTETRGRHPYLTAKDAEDLVVQSIAAYKAHHRHVPARLVVLKTSRFRSEEAEGIDAALGKSGIEMSDLVWVQESSPIAIFRDGNYPVLRGTFVDLDGKGLLYTRGSVPFYGTFPGLRVPRPLLLVPHENSDSTILTLAKDVLALTKVNWNTTQFDQKLPAPIKAAREVGRILKHVEFGTAVSSDFRRYT

Source

organism	Xanthobacter autotrophicus Py2
ncbi_taxonomy_id	78245
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	;DNA (5'-D(APTPTPCPGPGPCPCPGPTPGPTPAPCPAPAP*T)-3') ;
formula_weight	5202.4 kDa
src_method	syn
entity_count	8

Polymer

type	polydeoxyribonucleotide
strand_id	C,G,K,O,1,3,5,7

ATTCGGCCGTGTACAAT

Entity 4 polymer

description	;RNA (5'-R(PAPUPUPGPUPAPCPAPCPGPGPCPCPGPAPAP*U)-3') ;
formula_weight	5427.3 kDa
src_method	syn
entity_count	8

Polymer

type	polyribonucleotide
strand_id	D,H,L,P,2,4,6,8

AUUGUACACGGCCGAAU

Entity 5 polymer

description	dsDNA substrate, first strand
formula_weight	12994.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	S

ATAATGGTTTCTTAGACGTCGTTTTAGAGCTGTGTTGTTTCG

Entity 6 polymer

description	dsDNA substrate, second strand
formula_weight	12862.3 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

CGAAACAACACAGCTCTAAAACGACGTCTAAGAAACCATTAT

Entity 7 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	12

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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	3.00 Å
resolution_method	—
num_particles	204199

fit	/app/data/saxs_computation/qc/9qcc/9qcc.fit
pddf	/app/data/pr_computation/qc/9qcc/9qcc.pr.out
profile	/app/data/saxs_computation/qc/9qcc/9qcc.dat

Activated XauSPARDA filament assembly with bound dsDNA substrate

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

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)