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9pyo

Crystal structure of Fe/2-OG dependent dioxygenase MysH in complex with iron and 2-oxoglutarate

Method: X-RAY DIFFRACTION D_max: 54.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pyo
deposition_date	2025-08-08
last_revision	2026-05-06
title	Crystal structure of Fe/2-OG dependent dioxygenase MysH in complex with iron and 2-oxoglutarate
keywords	Non-heme iron dependent, dioxygenase, jelly roll fold, phytanoyl-CoA, alphaketoglutarate dependent, METAL BINDING PROTEIN; METAL 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	18.42 Å
rg_electron	17.22 Å
i0	14488900.00
molecular_weight	28905.0 kDa
excluded_volume	36243 Å³
envelope_volume	40344 Å³
shell_volume	19046 Å³
envelope_diameter	55.8 Å
shell_rg	23.98 Å
envelope_rg	17.49 Å
shape_rg	17.20 Å
total_rg	18.27 Å
total_atoms	2041
n_residues	249
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	54.3 Å
rg_real	18.27 Å
rg_real_error	0.23 Å
i0_real	1.4490e+07
i0_real_error	1.5470e+05
rg_reciprocal	18.29 Å
i0_reciprocal	14490000.0000
total_estimate	0.8308
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.5 Å
skewness	0.067
kurtosis	-0.498
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	4039000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.973; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Fe/2-OG dependent dioxygenase MysH
formula_weight	31051.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2260

SNAMLKVDTQKISPQQVEAFERDGVICVKNAVDDIWVERMRTAVDKNISIPGPLEDKNVPKPQGSAEHASSIWLIDADFRALAFESPLPTLAAQVLKSKKLNFLADGFFVKKPESNGRIGWHNDLPYWPVQGWQCCKIWLALDTVKQENGRLEYIKGSHQWGKELRERSNPSWFIEPEPHEILSWDMEAGDCLIHHFLTIHHSVTNISSTQRRAIVTNWTGDDVTYYQRPKAWPFKPLEEIDLPEFNSLKTKKSGEPIDCDIFPRVQVHR

Source

organism	Nostoc linckia
ncbi_taxonomy_id	92942
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	2-OXOGLUTARIC ACID
formula_weight	146.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

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

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	219

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6. Citations (1)

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length_a	44.495 Å
length_b	44.495 Å
length_c	107.316 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	3

space_group	P 31
int_tables_number	144
crystal_system	trigonal

resolution	1.500 Å
resolution_low	26.220 Å
r_factor	0.2091
r_work	0.2076
r_free	0.2365

fit	/app/data/saxs_computation/py/9pyo/9pyo.fit
pddf	/app/data/pr_computation/py/9pyo/9pyo.pr.out
profile	/app/data/saxs_computation/py/9pyo/9pyo.dat