← Back to search

9uad

Crystal structure of the OkaE-M64A mutant with a-ketoglutarate and okaramine A

Method: X-RAY DIFFRACTION D_max: 126.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9uad
deposition_date	2025-03-31
title	Crystal structure of the OkaE-M64A mutant with a-ketoglutarate and okaramine A
keywords	dioxygenase, non-heme, iron dependent, oxidoreductase; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	37.02 Å
rg_electron	36.62 Å
i0	536588000.00
molecular_weight	122450.0 kDa
excluded_volume	116850 Å³
envelope_volume	226110 Å³
shell_volume	51000 Å³
envelope_diameter	134.8 Å
shell_rg	43.32 Å
envelope_rg	35.90 Å
shape_rg	36.64 Å
total_rg	36.90 Å
total_atoms	9223
n_residues	1167
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

▼

3. P(r) Analysis (GNOM)

dmax	126.9 Å
rg_real	36.95 Å
rg_real_error	1.24 Å
i0_real	5.3660e+08
i0_real_error	9.5670e+06
rg_reciprocal	36.99 Å
i0_reciprocal	536600000.0000
total_estimate	0.8706
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.2 Å
skewness	0.265
kurtosis	-0.254
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	69570000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.947

▶

4. Crystallography & Experiment

▶

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	A,B,C,D
atom_count	9740

MGDRGPEFTLTENVMKPQIQRFTRDHDPKVLWQVVEEDGAVIIEGFLPHEVIQKFDCELDVRSKATKGGEANQEFYQMPVPTTTKWMNDLTATCPTFRHEILNNDILHSLCNVAFEPHGDYWLLNGMAMEMMPGNPTQQIHNDHGTHPILQYLRPDAPAPVFSIITAVTEFTESNGATRVILGSHRWPQGQKAKDDQAVRAALQPGDALVMHRSTKHGGAAHDADNQDHRRLLLTCMGTCQLAPYETNVTVPRPIVESMTPLAQKMIGWRSTRPVISNVTGLNTVRMKHLENQIELKSNVPLNVGGCWSHPQFEK

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	;(1Z,4R,12S,14S,17Z)-12-hydroxy-19,19-dimethyl-5-(2-methylbut-3-en-2-yl)-3,5,16,21-tetrazaheptacyclo[14.13.0.03,14.04,12.06,11.020,28.022,27]nonacosa-1(29),6,8,10,17,20(28),22,24,26-nonaene-2,15-dione ;
formula_weight	520.6 kDa
src_method	nat
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	517

▶

6. Citations (1)

▶

length_a	76.384 Å
length_b	107.709 Å
length_c	134.792 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	2.440 Å
resolution_low	38.730 Å
r_factor	0.1781
r_work	0.1752
r_free	0.2332

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