SAXSdb — 9w55

▼

1. Structure Basics

entry_id	9w55
deposition_date	2025-08-01
last_revision	2026-01-07
title	Structure of L-glutamate oxidase E617Q mutant
keywords	L-glutamic acid oxidase, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	25.90 Å
rg_electron	24.88 Å
i0	79200700.00
molecular_weight	68629.0 kDa
excluded_volume	85343 Å³
envelope_volume	101480 Å³
shell_volume	33295 Å³
envelope_diameter	89.3 Å
shell_rg	32.75 Å
envelope_rg	24.96 Å
shape_rg	24.88 Å
total_rg	25.69 Å
total_atoms	4854
n_residues	606
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	86.0 Å
rg_real	25.79 Å
rg_real_error	0.48 Å
i0_real	7.9200e+07
i0_real_error	1.1360e+06
rg_reciprocal	25.82 Å
i0_reciprocal	79200000.0000
total_estimate	0.8815
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.4 Å
skewness	0.245
kurtosis	-0.327
angular_range	— – 0.3050 Å⁻¹
current_alpha	0.0000
highest_alpha	15340000.0000
n_real_points	62
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.820; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.996

▶

4. Crystallography & Experiment

▶

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	5120

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	17451.1 kDa
ec_number	1.4.3.11
mutation	E617Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

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	1

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	266

▶

6. Citations (1)

▶

length_a	125.201 Å
length_b	125.201 Å
length_c	170.813 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	hexagonal

resolution	2.430 Å
resolution_low	58.780 Å
r_factor	0.1983
r_work	0.1965
r_free	0.2327

fit	/app/data/saxs_computation/w5/9w55/9w55.fit
pddf	/app/data/pr_computation/w5/9w55/9w55.pr.out
profile	/app/data/saxs_computation/w5/9w55/9w55.dat

Structure of L-glutamate oxidase E617Q 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 (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)