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9w56

Structure of L-glutamate oxidase E617Q mutant in complex with L-glutamate

Method: X-RAY DIFFRACTION D_max: 165.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9w56
deposition_date	2025-08-01
last_revision	2026-01-07
title	Structure of L-glutamate oxidase E617Q mutant in complex with L-glutamate
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	48.23 Å
rg_electron	48.62 Å
i0	1119690000.00
molecular_weight	274620.0 kDa
excluded_volume	341480 Å³
envelope_volume	434770 Å³
shell_volume	75331 Å³
envelope_diameter	171.4 Å
shell_rg	51.09 Å
envelope_rg	48.48 Å
shape_rg	48.62 Å
total_rg	48.71 Å
total_atoms	19424
n_residues	2425
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	165.3 Å
rg_real	48.67 Å
rg_real_error	1.67 Å
i0_real	1.1200e+09
i0_real_error	2.1120e+07
rg_reciprocal	48.24 Å
i0_reciprocal	1119000000.0000
total_estimate	0.8204
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	45.1 Å
skewness	0.492
kurtosis	-0.483
angular_range	— – 0.1650 Å⁻¹
current_alpha	0.0000
highest_alpha	487600000.0000
n_real_points	34
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.692; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.669

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	L-glutamate oxidase precursor
formula_weight	42019.2 kDa
ec_number	1.4.3.11
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,D,G,J
atom_count	20701

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	4

Polymer

type	polypeptide(L)
strand_id	B,E,H,K

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	17451.1 kDa
ec_number	1.4.3.11
mutation	E617Q
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,F,I,L

GGVRPATNAYGGGSTTDNPNRFMYYPSHPVPGTQGGVVLAAYSWSDDAARWDSFDDAERYGYALENLQSVHGRRIEVFYTGAGQTQSWLRDPYACGQAAVYTPHQMTAFHLDVVRPEGPVYFAGEHVSLKHAWIEGAVETAVRAAIAVNEAPVGDTGVTAAAG

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	4

Entity 5 non-polymer

description	GLUTAMIC ACID
formula_weight	147.1 kDa
src_method	syn
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1277

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6. Citations (1)

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length_a	85.957 Å
length_b	117.651 Å
length_c	147.953 Å
angle_alpha	90.00 °
angle_beta	105.16 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.380 Å
resolution_low	61.040 Å
r_factor	0.1766
r_work	0.1743
r_free	0.2202

fit	/app/data/saxs_computation/w5/9w56/9w56.fit
pddf	/app/data/pr_computation/w5/9w56/9w56.pr.out
profile	/app/data/saxs_computation/w5/9w56/9w56.dat

Structure of L-glutamate oxidase E617Q mutant in complex with L-glutamate

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)