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9rds

Protein with novel 3_1 knotted solenoid fold

Method: X-RAY DIFFRACTION D_max: 54.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rds
deposition_date	2025-06-03
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	16.28 Å
rg_electron	14.80 Å
i0	4382430.00
molecular_weight	14773.0 kDa
excluded_volume	18533 Å³
envelope_volume	22061 Å³
shell_volume	12764 Å³
envelope_diameter	55.8 Å
shell_rg	20.52 Å
envelope_rg	15.43 Å
shape_rg	14.75 Å
total_rg	16.16 Å
total_atoms	2074
n_residues	131
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	54.5 Å
rg_real	16.21 Å
rg_real_error	0.39 Å
i0_real	4.3820e+06
i0_real_error	5.0090e+04
rg_reciprocal	16.22 Å
i0_reciprocal	4382000.0000
total_estimate	0.7940
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	19.6 Å
skewness	0.247
kurtosis	-0.196
angular_range	— – 0.4900 Å⁻¹
current_alpha	0.0000
highest_alpha	717000.0000
n_real_points	79
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	A0A653LYW1
formula_weight	14965.0 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2315

QGIDPFTMKTILPINRPLADAPDLNAARFENVDIILYELYAAADAKGVPLVEGRTFTGCRFQGPAVILVSNGVTFTDTNFGDGRGSIKNLLTRSLGDKAIGTIPMRDCKFIGCEFYGVGFTGTDEFLDQVAALTDKPKA

Source

organism	Brevundimonas sp. G8
ncbi_taxonomy_id	1350776
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	9

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	146

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6. Citations (1)

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length_a	57.690 Å
length_b	57.690 Å
length_c	70.490 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	trigonal

resolution	1.220 Å
resolution_low	28.850 Å
r_factor	0.1312
r_work	0.1299
r_free	0.1562

fit	/app/data/saxs_computation/rd/9rds/9rds.fit
pddf	/app/data/pr_computation/rd/9rds/9rds.pr.out
profile	/app/data/saxs_computation/rd/9rds/9rds.dat