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9qbq

Crystal structure of apo SPARDA complex from Xanthobacter autotrophicus

Method: X-RAY DIFFRACTION D_max: 159.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qbq
deposition_date	2025-03-03
title	Crystal structure of apo SPARDA complex from Xanthobacter autotrophicus
keywords	Protein-nucleic acid interactions, Argonaute, pAgo, guide and target specificity, RNA BINDING PROTEIN; RNA BINDING PROTEIN
method	X-RAY DIFFRACTION

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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	42.26 Å
rg_electron	42.06 Å
i0	587185000.00
molecular_weight	196360.0 kDa
excluded_volume	245430 Å³
envelope_volume	337190 Å³
shell_volume	68683 Å³
envelope_diameter	171.7 Å
shell_rg	45.73 Å
envelope_rg	41.69 Å
shape_rg	42.04 Å
total_rg	42.31 Å
total_atoms	13851
n_residues	1729
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	159.0 Å
rg_real	42.44 Å
rg_real_error	1.88 Å
i0_real	5.8720e+08
i0_real_error	1.2010e+07
rg_reciprocal	42.26 Å
i0_reciprocal	587100000.0000
total_estimate	0.8129
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	47.3 Å
skewness	0.597
kurtosis	0.256
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	68120000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.549; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.948

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DUF4365 domain-containing protein
formula_weight	52420.3 kDa
mutation	N-terminal His-tag
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	13859

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	2

Polymer

type	polypeptide(L)
strand_id	B,D

MTFKAHVFDEPMLEFGDGGQHCDPRQGLREHGPLQPRSGDVIRVGVIGTDDTVAGFTEFLAETGRGIESGNKQLINLNPDFPGLGNQNPFRCKFEVPDGATVTISRRQVNDITGIGRHDEAVRHAVELISSQLSALVEGSAKPDVIVLALPIPLIEKLVNAKSEGEDSDDDVDGGDMLNFRDLLKAKTLHLPVPTQIVWPDTWDDAAKIPRKIKRDSNRQTQVKATRAWNLLNALFYKAGKVPWRLLPDQAEYRTSFLGIGFYRDLDGQQLWTSTAQMFDERGRGLILRGARAQTETRGRHPYLTAKDAEDLVVQSIAAYKAHHRHVPARLVVLKTSRFRSEEAEGIDAALGKSGIEMSDLVWVQESSPIAIFRDGNYPVLRGTFVDLDGKGLLYTRGSVPFYGTFPGLRVPRPLLLVPHENSDSTILTLAKDVLALTKVNWNTTQFDQKLPAPIKAAREVGRILKHVEFGTAVSSDFRRYT

Source

organism	Xanthobacter autotrophicus Py2
ncbi_taxonomy_id	78245
host_organism	Escherichia coli

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	16

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	8

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6. Citations (1)

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length_a	127.734 Å
length_b	73.290 Å
length_c	128.001 Å
angle_alpha	90.00 °
angle_beta	115.17 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	3.000 Å
resolution_low	68.550 Å
r_factor	0.2355
r_work	0.2304
r_free	0.2817

fit	/app/data/saxs_computation/qb/9qbq/9qbq.fit
pddf	/app/data/pr_computation/qb/9qbq/9qbq.pr.out
profile	/app/data/saxs_computation/qb/9qbq/9qbq.dat

Crystal structure of apo SPARDA complex from Xanthobacter autotrophicus

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

Refinement

Diffraction

5. Entities & Polymer Info (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)