SAXSdb — 9w54

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1. Structure Basics

entry_id	9w54
deposition_date	2025-08-01
last_revision	2026-01-07
title	Structure of L-glutamate oxidase 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	25.68 Å
rg_electron	24.68 Å
i0	79561100.00
molecular_weight	68855.0 kDa
excluded_volume	85595 Å³
envelope_volume	100470 Å³
shell_volume	33123 Å³
envelope_diameter	88.1 Å
shell_rg	32.77 Å
envelope_rg	24.84 Å
shape_rg	24.68 Å
total_rg	25.50 Å
total_atoms	4870
n_residues	608
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	84.1 Å
rg_real	25.59 Å
rg_real_error	0.48 Å
i0_real	7.9560e+07
i0_real_error	1.0500e+06
rg_reciprocal	25.62 Å
i0_reciprocal	79560000.0000
total_estimate	0.8859
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.2 Å
skewness	0.265
kurtosis	-0.317
angular_range	— – 0.3100 Å⁻¹
current_alpha	0.0000
highest_alpha	16080000.0000
n_real_points	63
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.991

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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	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5089

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	1

Polymer

type	polypeptide(L)
strand_id	B

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	17452.1 kDa
ec_number	1.4.3.11
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

GGVRPATNAYGGGSTTDNPNRFMYYPSHPVPGTQGGVVLAAYSWSDDAARWDSFDDAERYGYALENLQSVHGRRIEVFYTGAGQTQSWLRDPYACGEAAVYTPHQMTAFHLDVVRPEGPVYFAGEHVSLKHAWIEGAVETAVRAAIAVNEAPVGDTGVTAAAG

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	1

Entity 5 non-polymer

description	GLUTAMIC ACID
formula_weight	147.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	219

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6. Citations (1)

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length_a	124.310 Å
length_b	124.310 Å
length_c	168.801 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 61 2 2
int_tables_number	178
crystal_system	—

resolution	2.550 Å
resolution_low	62.150 Å
r_factor	0.1962
r_work	0.1921
r_free	0.2465

fit	/app/data/saxs_computation/w5/9w54/9w54.fit
pddf	/app/data/pr_computation/w5/9w54/9w54.pr.out
profile	/app/data/saxs_computation/w5/9w54/9w54.dat

Structure of L-glutamate oxidase 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)