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9u3e

Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254A mutant

Method: X-RAY DIFFRACTION D_max: 91.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u3e
deposition_date	2025-03-18
title	Monomeric sarcosine oxidase from Bacillus sp. (SoxB) Y254A mutant
keywords	Sarcosine 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	29.11 Å
rg_electron	28.31 Å
i0	119630000.00
molecular_weight	85893.0 kDa
excluded_volume	107030 Å³
envelope_volume	125250 Å³
shell_volume	35813 Å³
envelope_diameter	99.5 Å
shell_rg	36.43 Å
envelope_rg	28.52 Å
shape_rg	28.30 Å
total_rg	29.08 Å
total_atoms	6058
n_residues	760
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	91.7 Å
rg_real	29.05 Å
rg_real_error	0.66 Å
i0_real	1.1960e+08
i0_real_error	1.6940e+06
rg_reciprocal	29.08 Å
i0_reciprocal	119600000.0000
total_estimate	0.9024
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	30.6 Å
skewness	0.247
kurtosis	-0.536
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	47990000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.923

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Monomeric sarcosine oxidase
formula_weight	43982.3 kDa
ec_number	1.5.3.1
mutation	Y254A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6916

STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYAGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKTTIGSHHHHHH

Source

organism	Bacillus sp. B-0618
ncbi_taxonomy_id	69000
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	683

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6. Citations (1)

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length_a	72.776 Å
length_b	69.700 Å
length_c	73.665 Å
angle_alpha	90.00 °
angle_beta	93.75 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.350 Å
resolution_low	42.408 Å
r_factor	—
r_work	0.1554
r_free	0.1776

fit	/app/data/saxs_computation/u3/9u3e/9u3e.fit
pddf	/app/data/pr_computation/u3/9u3e/9u3e.pr.out
profile	/app/data/saxs_computation/u3/9u3e/9u3e.dat