SAXSdb — 9w57

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1. Structure Basics

entry_id	9w57
deposition_date	2025-08-01
last_revision	2026-01-07
title	Structure of L-glutamate oxidase E617F 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	31.45 Å
rg_electron	30.55 Å
i0	298660000.00
molecular_weight	136890.0 kDa
excluded_volume	170330 Å³
envelope_volume	203060 Å³
shell_volume	52166 Å³
envelope_diameter	102.6 Å
shell_rg	40.03 Å
envelope_rg	30.71 Å
shape_rg	30.55 Å
total_rg	31.31 Å
total_atoms	9684
n_residues	1210
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	96.0 Å
rg_real	31.25 Å
rg_real_error	0.47 Å
i0_real	2.9870e+08
i0_real_error	4.1850e+06
rg_reciprocal	31.33 Å
i0_reciprocal	298700000.0000
total_estimate	0.9013
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	40.3 Å
skewness	0.167
kurtosis	-0.489
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	104200000.0000
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: 0.955

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	9911

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	17470.1 kDa
ec_number	1.4.3.11
mutation	E617F
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

GGVRPATNAYGGGSTTDNPNRFMYYPSHPVPGTQGGVVLAAYSWSDDAARWDSFDDAERYGYALENLQSVHGRRIEVFYTGAGQTQSWLRDPYACGFAAVYTPHQMTAFHLDVVRPEGPVYFAGEHVSLKHAWIEGAVETAVRAAIAVNEAPVGDTGVTAAAG

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

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6. Citations (1)

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length_a	81.630 Å
length_b	150.260 Å
length_c	150.260 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 2 21 21
int_tables_number	18
crystal_system	orthorhombic

resolution	3.270 Å
resolution_low	81.630 Å
r_factor	0.1718
r_work	0.1685
r_free	0.2359

fit	/app/data/saxs_computation/w5/9w57/9w57.fit
pddf	/app/data/pr_computation/w5/9w57/9w57.pr.out
profile	/app/data/saxs_computation/w5/9w57/9w57.dat

Structure of L-glutamate oxidase E617F 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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)