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9u3d

Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with D-Proline

Method: X-RAY DIFFRACTION D_max: 89.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9u3d
deposition_date	2025-03-18
title	Monomeric sarcosine oxidase from Bacillus sp. (SoxB) complexed with D-Proline
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	28.28 Å
i0	123156000.00
molecular_weight	86682.0 kDa
excluded_volume	107810 Å³
envelope_volume	125610 Å³
shell_volume	35953 Å³
envelope_diameter	93.0 Å
shell_rg	36.46 Å
envelope_rg	28.47 Å
shape_rg	28.27 Å
total_rg	29.07 Å
total_atoms	6108
n_residues	759
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	89.4 Å
rg_real	29.05 Å
rg_real_error	0.61 Å
i0_real	1.2320e+08
i0_real_error	1.8230e+06
rg_reciprocal	29.08 Å
i0_reciprocal	123200000.0000
total_estimate	0.8976
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.5 Å
skewness	0.237
kurtosis	-0.548
angular_range	— – 0.2700 Å⁻¹
current_alpha	0.0000
highest_alpha	53030000.0000
n_real_points	55
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.812

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Monomeric sarcosine oxidase
formula_weight	44074.4 kDa
ec_number	1.5.3.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6764

STHFDVIVVGAGSMGMAAGYQLAKQGVKTLLVDAFDPPHTNGSHHGDTRIIRHAYGEGREYVPLALRSQELWYELEKETHHKIFTKTGVLVFGPKGESAFVAETMEAAKEHSLTVDLLEGDEINKRWPGITVPENYNAIFEPNSGVLFSENCIRAYRELAEARGAKVLTHTRVEDFDISPDSVKIETANGSYTADKLIVSMGAWNSKLLSKLNLDIPLQPYRQVVGFFESDESKYSNDIDFPGFMVEVPNGIYYGFPSFGGCGLKLGYHTFGQKIDPDTINREFGVYPEDESNLRAFLEEYMPGANGELKRGAVCMYTKTLDEHFIIDLHPEHSNVVIAAGFSGHGFKFSSGVGEVLSQLALTGKTEHDISIFSINRPALKESLQKTTIGSHHHHHH

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	D-PROLINE
formula_weight	115.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	458

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6. Citations (1)

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length_a	71.367 Å
length_b	69.687 Å
length_c	73.095 Å
angle_alpha	90.00 °
angle_beta	92.10 °
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	41.670 Å
r_factor	—
r_work	0.1579
r_free	0.1828

fit	/app/data/saxs_computation/u3/9u3d/9u3d.fit
pddf	/app/data/pr_computation/u3/9u3d/9u3d.pr.out
profile	/app/data/saxs_computation/u3/9u3d/9u3d.dat