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9pze

Crystal structure of Fe/2-OG dependent dioxygenase MysH with docked C-terminus

Method: X-RAY DIFFRACTION D_max: 110.5 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9pze
deposition_date	2025-08-11
last_revision	2026-05-06
title	Crystal structure of Fe/2-OG dependent dioxygenase MysH with docked C-terminus
keywords	Non-heme iron dependent, dioxygenase, jelly roll fold, phytanoyl-CoA, dioxygenase family protein, 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	31.37 Å
rg_electron	30.82 Å
i0	54831800.00
molecular_weight	58570.0 kDa
excluded_volume	73248 Å³
envelope_volume	95263 Å³
shell_volume	25781 Å³
envelope_diameter	117.1 Å
shell_rg	37.66 Å
envelope_rg	30.59 Å
shape_rg	30.82 Å
total_rg	31.47 Å
total_atoms	4140
n_residues	502
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	110.5 Å
rg_real	31.55 Å
rg_real_error	1.01 Å
i0_real	5.4830e+07
i0_real_error	8.7940e+05
rg_reciprocal	31.48 Å
i0_reciprocal	54830000.0000
total_estimate	0.7464
solution_quality	REASONABLE a REASONABLE solution
n_peaks	4
r_peak_primary	26.0 Å
skewness	0.322
kurtosis	-0.722
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	20530000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.437; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.457; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Fe/2-OG dependent dioxygenase MysH
formula_weight	31782.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4547

MLKVDTQKISPQQVEAFERDGVICVKNAVDDIWVERMRTAVDKNISIPGPLEDKNVPKPQGSAEHASSIWLIDADFRALAFESPLPTLAAQVLKSKKLNFLADGFFVKKPESNGRIGWHNDLPYWPVQGWQCCKIWLALDTVKQENGRLEYIKGSHQWGKELRERSNPSWFIEPEPHEILSWDMEAGDCLIHHFLTIHHSVTNISSTQRRAIVTNWTGDDVTYYQRPKAWPFKPLEEIDLPEFNSLKTKKSGEPIDCDIFPRVQVHRSSHHHHHH

Source

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

Entity 2 non-polymer

description	CITRATE ANION
formula_weight	189.1 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	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	407

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6. Citations (1)

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length_a	88.505 Å
length_b	142.701 Å
length_c	44.612 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 2
int_tables_number	18
crystal_system	orthorhombic

resolution	1.680 Å
resolution_low	41.900 Å
r_factor	0.1825
r_work	0.1808
r_free	0.2152

fit	/app/data/saxs_computation/pz/9pze/9pze.fit
pddf	/app/data/pr_computation/pz/9pze/9pze.pr.out
profile	/app/data/saxs_computation/pz/9pze/9pze.dat

Crystal structure of Fe/2-OG dependent dioxygenase MysH with docked C-terminus

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