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9s59

diFe-Sulerythin_E53D O2-reacted

Method: X-RAY DIFFRACTION D_max: 62.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s59
deposition_date	2025-07-29
last_revision	2026-06-10
title	diFe-Sulerythin_E53D O2-reacted
keywords	dioxygen activation, four-helix bundle, diiron, diferric-peroxo ligand, OXIDOREDUCTASE; OXIDOREDUCTASE
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	19.98 Å
rg_electron	19.19 Å
i0	18772700.00
molecular_weight	32318.0 kDa
excluded_volume	40109 Å³
envelope_volume	44774 Å³
shell_volume	19468 Å³
envelope_diameter	65.7 Å
shell_rg	25.34 Å
envelope_rg	19.47 Å
shape_rg	19.18 Å
total_rg	20.04 Å
total_atoms	4458
n_residues	286
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	62.9 Å
rg_real	19.87 Å
rg_real_error	0.30 Å
i0_real	1.8770e+07
i0_real_error	2.2250e+05
rg_reciprocal	19.88 Å
i0_reciprocal	18770000.0000
total_estimate	0.9042
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	23.9 Å
skewness	0.140
kurtosis	-0.579
angular_range	— – 0.4000 Å⁻¹
current_alpha	0.0000
highest_alpha	5358000.0000
n_real_points	72
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.924; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Sulerythrin
formula_weight	16222.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4758

HMKDLKGTKTAENLKQGFIGESMANRRYLYFAKRADEEGYPEIAGLLRSIAEGDTAHAFGHLDFIRQGGLTDPATDKPIGTLEQMIESAIAGETYEWTQMYPGFAKVAREEGFPEVAEWFETLARAEKSHAEKFQNVLKQLKGGT

Source

organism	Sulfurisphaera tokodaii str. 7
ncbi_taxonomy_id	273063
host_organism	Escherichia coli B

Entity 2 non-polymer

description	PEROXIDE ION
formula_weight	32.0 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	202

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6. Citations (1)

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length_a	72.150 Å
length_b	72.150 Å
length_c	98.260 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	—

resolution	1.760 Å
resolution_low	38.620 Å
r_factor	0.1695
r_work	0.1675
r_free	0.2083

fit	/app/data/saxs_computation/s5/9s59/9s59.fit
pddf	/app/data/pr_computation/s5/9s59/9s59.pr.out
profile	/app/data/saxs_computation/s5/9s59/9s59.dat