SAXSdb — 9qbp

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1. Structure Basics

entry_id	9qbp
deposition_date	2025-03-03
title	Crystal structure of Enhydrobacter aerosaccus apo SPARDA complex
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	40.40 Å
rg_electron	40.02 Å
i0	505381000.00
molecular_weight	184880.0 kDa
excluded_volume	232370 Å³
envelope_volume	311440 Å³
shell_volume	65744 Å³
envelope_diameter	156.1 Å
shell_rg	45.06 Å
envelope_rg	39.40 Å
shape_rg	40.00 Å
total_rg	40.36 Å
total_atoms	13061
n_residues	1631
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	142.6 Å
rg_real	40.47 Å
rg_real_error	1.36 Å
i0_real	5.0540e+08
i0_real_error	9.5710e+06
rg_reciprocal	40.40 Å
i0_reciprocal	505300000.0000
total_estimate	0.8413
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	47.5 Å
skewness	0.495
kurtosis	0.053
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	53110000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.856

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DUF4365 domain-containing protein
formula_weight	53186.8 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	13521

MGGSHHHHHHGMASENLYFQGGTKTITDSQVLGELGETAVKKIVLETGFIYEHRGRLEAGTDGLIELRDPKSGAPLGKLLAVQVKATKESQYLRETDKGFEYLLRPADLKLWRLSNIPVIIVLWRQSDGSAYWKDVTDSVRGEERRLQFDKAADVFDPGCADRLGALTVDRRKPGVFVPPLNGGETAIINLLRIKLPEEIFIATSPFGSGRDAVPELLKHSNTRFDWVIRKRRYVSFFDPREYGTKAIVDVDQVEAIDSDIFAFNDDLDDTNDTMDLLRRTVERQLSAQVSYLRKERLFYFHAVATNKSRSYRYLANVKETSAKVVSAYTNKKNPEGRGYVRHHAATFRFERLADEWFVVVDPTFYFTNDGFRPHRYPEALLAGKKRLERNAAVRGQVVMWQHLLVESASCNNGLFDQNEHADVLLDFENLPVIELSRAVPESSWTRTDPRAKEMESRDLFDEGGAA

Source

organism	Enhydrobacter aerosaccus
ncbi_taxonomy_id	225324
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Protein argonaute
formula_weight	54131.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

MILKSRVFDEPMLEFGDGGQHLDPRQGLREYGPLQPRSGDVVHVGVIGTEDTIAGFSEFLAETAAGIDSDNKQLINLNPDFPGLGNQNPFRCKFVIPDGATATISRRQVTEIKQIGRHDEAVRRAVALIADQLSALMESSAKPDVIVLALPVPLIEKLVNAKSEEIADIAEDEENRDDTLNFRDLLKAKTLHLDVPTQIVWPDTWDDAAKIPRKVKRDSNRQTQAKATRAWNLLNALFYKAGKVPWRLLPDQAEYRTSFLGIGFYRDLDGQQLWTSTAQMFDERGRGLILRGARAQTETKGRHPYLTAKDADDLVTQSIAAYKAHHKHVPARVVVLKTSRFRPEEAEGIDSALSRLGIELSDLVWVQESSPIAVFRDGNYPILRGTFVDLKGKGLLYTRGSVPYYGTYPGLRVPRPLLLVPHENSDSALARLAEEVLALTKVNWNTTQFDQKLPAPIKAAREVGRILKHIEYGVAISPDFRKYT

Source

organism	Enhydrobacter aerosaccus
ncbi_taxonomy_id	225324
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	7

Entity 4 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	BETA-MERCAPTOETHANOL
formula_weight	78.1 kDa
src_method	syn
entity_count	3

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	386

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6. Citations (1)

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length_a	108.179 Å
length_b	127.241 Å
length_c	191.336 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.450 Å
resolution_low	94.170 Å
r_factor	0.2092
r_work	0.2049
r_free	0.2479

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

Crystal structure of Enhydrobacter aerosaccus apo SPARDA complex

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)