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9uae

Crystal structure of the OkaE-M71A mutant with coblat(II)

Method: X-RAY DIFFRACTION D_max: 111.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uae
deposition_date	2025-03-31
title	Crystal structure of the OkaE-M71A mutant with coblat(II)
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	34.40 Å
rg_electron	33.61 Å
i0	285629000.00
molecular_weight	131760.0 kDa
excluded_volume	163110 Å³
envelope_volume	206120 Å³
shell_volume	50001 Å³
envelope_diameter	111.6 Å
shell_rg	41.33 Å
envelope_rg	33.40 Å
shape_rg	33.61 Å
total_rg	34.12 Å
total_atoms	9229
n_residues	1169
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	111.8 Å
rg_real	34.32 Å
rg_real_error	0.68 Å
i0_real	2.8560e+08
i0_real_error	4.7340e+06
rg_reciprocal	34.37 Å
i0_reciprocal	285600000.0000
total_estimate	0.6923
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	109.4 Å
skewness	0.227
kurtosis	-0.491
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	95270000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 0.122; Positv: 1.000; Valcen: 0.999; Smooth: 0.918

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Iron/alpha-ketoglutarate-dependent dioxygenase okaE
formula_weight	35439.2 kDa
ec_number	1.14.-.-
mutation	M71A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,D,A,B
atom_count	9758

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	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	12

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	529

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6. Citations (1)

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length_a	76.150 Å
length_b	107.663 Å
length_c	134.428 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	2.400 Å
resolution_low	38.620 Å
r_factor	0.2001
r_work	0.1981
r_free	0.2375

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

Crystal structure of the OkaE-M71A mutant with coblat(II)

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