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9qix

Protein with novel 3_1 knotted solenoid fold

Method: X-RAY DIFFRACTION D_max: 53.2 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qix
deposition_date	2025-03-17
title	Protein with novel 3_1 knotted solenoid fold
keywords	3_1 Knot, Novel Fold, Solenoid, Brevundimonas sp., UNKNOWN FUNCTION; UNKNOWN FUNCTION
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	20.46 Å
rg_electron	19.34 Å
i0	14576600.00
molecular_weight	29346.0 kDa
excluded_volume	37051 Å³
envelope_volume	43706 Å³
shell_volume	19252 Å³
envelope_diameter	89.5 Å
shell_rg	25.46 Å
envelope_rg	20.12 Å
shape_rg	19.32 Å
total_rg	20.30 Å
total_atoms	4138
n_residues	262
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	53.2 Å
rg_real	19.32 Å
rg_real_error	0.06 Å
i0_real	1.3870e+07
i0_real_error	1.2690e+05
rg_reciprocal	20.49 Å
i0_reciprocal	14580000.0000
total_estimate	0.6855
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	23.6 Å
skewness	0.142
kurtosis	-0.478
angular_range	— – 0.3900 Å⁻¹
current_alpha	2.4750
highest_alpha	1880000.0000
n_real_points	71
gnom_version	4.1.3
quality_criteria	AN1: 0.004; Oscil: 0.992; Stabil: 0.980; Sysdev: 0.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	A0A2W6Z6R8
formula_weight	14884.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4554

QGIDPFTMKSILPINRPLTDAPDLNATTFENVDIILYELFTAAAAKGVPLIEGRTFRGCRFQGPAIVLASTGVTFSDTNFGESRGGIANLLLRPVGDKAIGTIPMRDCHFIGCEFYGVGFTGPESFIAEVSTLTDKPKA

Source

organism	Brevundimonas sp.
ncbi_taxonomy_id	1871086
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	17

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

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	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	287

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6. Citations (1)

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length_a	133.390 Å
length_b	133.390 Å
length_c	53.380 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 63
int_tables_number	173
crystal_system	hexagonal

resolution	1.660 Å
resolution_low	32.040 Å
r_factor	0.1566
r_work	0.1559
r_free	0.1802

fit	/app/data/saxs_computation/qi/9qix/9qix.fit
pddf	/app/data/pr_computation/qi/9qix/9qix.pr.out
profile	/app/data/saxs_computation/qi/9qix/9qix.dat