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9uah

Crystal structure of the OkaE-W79A mutant with a-ketoglutarate and okaramine A

Method: X-RAY DIFFRACTION D_max: 123.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9uah
deposition_date	2025-03-31
title	Crystal structure of the OkaE-W79A mutant with a-ketoglutarate and okaramine A
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	34.31 Å
rg_electron	33.78 Å
i0	526240000.00
molecular_weight	120800.0 kDa
excluded_volume	115140 Å³
envelope_volume	199550 Å³
shell_volume	48624 Å³
envelope_diameter	129.4 Å
shell_rg	40.87 Å
envelope_rg	33.53 Å
shape_rg	33.77 Å
total_rg	34.16 Å
total_atoms	9093
n_residues	1150
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	123.4 Å
rg_real	34.28 Å
rg_real_error	0.94 Å
i0_real	5.2620e+08
i0_real_error	9.3150e+06
rg_reciprocal	34.30 Å
i0_reciprocal	526200000.0000
total_estimate	0.8608
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	37.5 Å
skewness	0.317
kurtosis	-0.345
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0004
highest_alpha	184200000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.738; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.996

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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	35384.2 kDa
ec_number	1.14.-.-
mutation	W79A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,A,C,D
atom_count	9615

MGDRGPEFTLTENVMKPQIQRFTRDHDPKVLWQVVEEDGAVIIEGFLPHEVIQKFDCELDVRSKATKGGEMNQEFYQMPVPTTTKAMNDLTATCPTFRHEILNNDILHSLCNVAFEPHGDYWLLNGMAMEMMPGNPTQQIHNDHGTHPILQYLRPDAPAPVFSIITAVTEFTESNGATRVILGSHRWPQGQKAKDDQAVRAALQPGDALVMHRSTKHGGAAHDADNQDHRRLLLTCMGTCQLAPYETNVTVPRPIVESMTPLAQKMIGWRSTRPVISNVTGLNTVRMKHLENQIELKSNVPLNVGGCWSHPQFEK

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	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	522

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6. Citations (1)

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length_a	75.775 Å
length_b	116.368 Å
length_c	127.139 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	2.500 Å
resolution_low	48.700 Å
r_factor	0.1766
r_work	0.1741
r_free	0.2250

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