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9uaf

Crystal structure of the OkaE-M71A mutant with a-ketoglutarate

Method: X-RAY DIFFRACTION D_max: 112.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uaf
deposition_date	2025-03-31
title	Crystal structure of the OkaE-M71A mutant with a-ketoglutarate
keywords	dioxygenase, non-heme, iron dependent, 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	34.46 Å
rg_electron	33.66 Å
i0	280907000.00
molecular_weight	130650.0 kDa
excluded_volume	161660 Å³
envelope_volume	204000 Å³
shell_volume	49497 Å³
envelope_diameter	114.9 Å
shell_rg	41.27 Å
envelope_rg	33.46 Å
shape_rg	33.67 Å
total_rg	34.17 Å
total_atoms	9156
n_residues	1166
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	112.8 Å
rg_real	34.38 Å
rg_real_error	0.66 Å
i0_real	2.8090e+08
i0_real_error	3.9800e+06
rg_reciprocal	34.43 Å
i0_reciprocal	280900000.0000
total_estimate	0.8940
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	41.7 Å
skewness	0.235
kurtosis	-0.478
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0001
highest_alpha	94380000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.931

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Iron/alpha-ketoglutarate-dependent dioxygenase okaE
formula_weight	35439.2 kDa
ec_number	1.14.-.-
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,D,A,B
atom_count	9612

MGDRGPEFTLTENVMKPQIQRFTRDHDPKVLWQVVEEDGAVIIEGFLPHEVIQKFDCELDVRSKATKGGEMNQEFYQAPVPTTTKWMNDLTATCPTFRHEILNNDILHSLCNVAFEPHGDYWLLNGMAMEMMPGNPTQQIHNDHGTHPILQYLRPDAPAPVFSIITAVTEFTESNGATRVILGSHRWPQGQKAKDDQAVRAALQPGDALVMHRSTKHGGAAHDADNQDHRRLLLTCMGTCQLAPYETNVTVPRPIVESMTPLAQKMIGWRSTRPVISNVTGLNTVRMKHLENQIELKSNVPLNVGGCWSHPQFEK

Source

organism	Penicillium simplicissimum
ncbi_taxonomy_id	69488
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	COBALT (II) ION
formula_weight	58.9 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	2-OXOGLUTARIC ACID
formula_weight	146.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	nat
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	456

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6. Citations (1)

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length_a	76.415 Å
length_b	107.826 Å
length_c	134.587 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.540 Å
resolution_low	38.730 Å
r_factor	0.1878
r_work	0.1850
r_free	0.2407

fit	/app/data/saxs_computation/ua/9uaf/9uaf.fit
pddf	/app/data/pr_computation/ua/9uaf/9uaf.pr.out
profile	/app/data/saxs_computation/ua/9uaf/9uaf.dat