SAXSdb — 9w58

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1. Structure Basics

entry_id	9w58
deposition_date	2025-08-01
last_revision	2026-01-07
title	Structure of L-glutamate oxidase E617K mutant
keywords	L-glutamic acid oxidase, 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	31.39 Å
rg_electron	30.49 Å
i0	300621000.00
molecular_weight	137390.0 kDa
excluded_volume	170980 Å³
envelope_volume	203530 Å³
shell_volume	52269 Å³
envelope_diameter	102.4 Å
shell_rg	40.11 Å
envelope_rg	30.70 Å
shape_rg	30.49 Å
total_rg	31.24 Å
total_atoms	9718
n_residues	1214
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	95.8 Å
rg_real	31.19 Å
rg_real_error	0.50 Å
i0_real	3.0060e+08
i0_real_error	4.5960e+06
rg_reciprocal	31.28 Å
i0_reciprocal	300600000.0000
total_estimate	0.9016
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.3 Å
skewness	0.163
kurtosis	-0.495
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	106300000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.960

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	L-glutamate oxidase precursor
formula_weight	42019.2 kDa
ec_number	1.4.3.11
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	11387

ANEMTYEQLARELLLVGPAPTNEDLKLRYLDVLIDNGLNPPGPPKRILIVGAGIAGLVAGDLLTRAGHDVTILEANANRVGGRIKTFHAKKGEPSPFADPAQYAEAGAMRLPSFHPLTLALIDKLGLKRRLFFNVDIDPQTGNQDAPVPPVFYKSFKDGKTWTNGAPSPEFKEPDKRNHTWIRTNREQVRRAQYATDPSSINEGFHLTGCETRLTVSDMVNQALEPVRDYYSVKQDDGTRVNKPFKEWLAGWADVVRDFDGYSMGRFLREYAEFSDEAVEAIGTIENMTSRLHLAFFHSFLGRSDIDPRATYWEIEGGSRMLPETLAKDLRDQIVMGQRMVRLEYYDPGRDGHHGELTGPGGPAVAIQTVPEGEPY

Source

organism	Streptomyces sp. X-119-6
ncbi_taxonomy_id	196112
host_organism	Escherichia coli

Entity 2 polymer

description	L-glutamate oxidase precursor
formula_weight	10575.8 kDa
ec_number	1.4.3.11
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

AATQTWTGDLAIVTIPFSSLRFVKVTPPFSYKKRRAVIETHYDQATKVLLEFSRRWWEFTEADWKRELDAIAPGLYDYYQQWGEDDAEAA

Source

organism	Streptomyces sp. X-119-6
ncbi_taxonomy_id	196112
host_organism	Escherichia coli

Entity 3 polymer

description	L-glutamate oxidase precursor
formula_weight	19354.2 kDa
ec_number	1.4.3.11
mutation	E617K
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

GGVRPATNAYGGGSTTDNPNRFMYYPSHPVPGTQGGVVLAAYSWSDDAARWDSFDDAERYGYALENLQSVHGRRIEVFYTGAGQTQSWLRDPYACGKAAVYTPHQMTAFHLDVVRPEGPVYFAGEHVSLKHAWIEGAVETAVRAAIAVNEAPVGDTGVTAAAGRRGAAAATEPMREEALTS

Source

organism	Streptomyces sp. X-119-6
ncbi_taxonomy_id	196112
host_organism	Escherichia coli

Entity 4 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1467

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6. Citations (1)

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length_a	68.800 Å
length_b	128.900 Å
length_c	150.780 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	1.850 Å
resolution_low	65.080 Å
r_factor	0.1543
r_work	0.1526
r_free	0.1871

fit	/app/data/saxs_computation/w5/9w58/9w58.fit
pddf	/app/data/pr_computation/w5/9w58/9w58.pr.out
profile	/app/data/saxs_computation/w5/9w58/9w58.dat

Structure of L-glutamate oxidase E617K mutant

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

5. Entities & Polymer Info (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)