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9vkm

Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase MicC

Method: X-RAY DIFFRACTION D_max: 92.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vkm
deposition_date	2025-06-23
last_revision	2026-04-29
title	Crystal structure of the Fe(II)/alpha-ketoglutarate dependent dioxygenase MicC
keywords	Oxidoreductase, Alpha-ketoglutarate-dependent enzyme, RiPP biosynthesis; 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	28.42 Å
rg_electron	28.08 Å
i0	65568200.00
molecular_weight	65422.0 kDa
excluded_volume	82604 Å³
envelope_volume	97656 Å³
shell_volume	29814 Å³
envelope_diameter	100.3 Å
shell_rg	34.40 Å
envelope_rg	28.12 Å
shape_rg	28.08 Å
total_rg	28.73 Å
total_atoms	4621
n_residues	567
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	92.5 Å
rg_real	28.57 Å
rg_real_error	0.74 Å
i0_real	6.5570e+07
i0_real_error	9.7510e+05
rg_reciprocal	28.53 Å
i0_reciprocal	65570000.0000
total_estimate	0.7990
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.1 Å
skewness	0.440
kurtosis	-0.443
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	25470000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.924; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Alpha-ketoglutarate-dependent non-heme iron oxygenase MicC Chain A
formula_weight	33653.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	4894

MGSSHHHHHHSSGLVPRGSHMITEGVKLFLNNSSDIADRLYLSSGLQHMQDSSTDGYAYYKYAVIPKSPWSLAAGSTKKYLVTHQKPPIEEFSKNIIILTLPDELIDFVQKAGISDFKNKEEVLAFNQTPTFIEASEKLKAFACQYLFSPSRFSCYHFFVEKPDLSVVTIGERKERMGMHIDNRGGVNIKDAELAPNIFLMNLGREDRYFIYINQPLETVKKMIETKNGAALDEFSNESLQYKFYQAFPDYPVVKIRIKPFECYIAPAENIIHDGSTEGNTNPSVKFLLEGYFWS

Source

organism	Mucilaginibacter inviolabilis
ncbi_taxonomy_id	2714892
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

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

Entity 4 non-polymer

description	CITRIC ACID
formula_weight	192.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	264

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6. Citations (1)

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length_a	61.319 Å
length_b	131.163 Å
length_c	132.248 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

resolution	2.200 Å
resolution_low	93.130 Å
r_factor	0.1680
r_work	0.1663
r_free	0.2014

fit	/app/data/saxs_computation/vk/9vkm/9vkm.fit
pddf	/app/data/pr_computation/vk/9vkm/9vkm.pr.out
profile	/app/data/saxs_computation/vk/9vkm/9vkm.dat