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9thy

ReAIV structure containing an acrylamide adduct at Cys183 and an orthoborate ester at Ser47

Method: X-RAY DIFFRACTION D_max: 86.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9thy
deposition_date	2025-12-04
last_revision	2026-05-27
title	ReAIV structure containing an acrylamide adduct at Cys183 and an orthoborate ester at Ser47
keywords	L-asparaginase, acrylamide, zinc metalloenzyme, adduct, microcalorimetry, ITC, HYDROLASE; HYDROLASE
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	27.12 Å
rg_electron	26.40 Å
i0	93543400.00
molecular_weight	72906.0 kDa
excluded_volume	89888 Å³
envelope_volume	106050 Å³
shell_volume	33279 Å³
envelope_diameter	90.4 Å
shell_rg	34.27 Å
envelope_rg	26.24 Å
shape_rg	26.42 Å
total_rg	27.07 Å
total_atoms	5066
n_residues	676
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	86.7 Å
rg_real	27.10 Å
rg_real_error	0.65 Å
i0_real	9.3540e+07
i0_real_error	1.5260e+06
rg_reciprocal	27.11 Å
i0_reciprocal	93540000.0000
total_estimate	0.8975
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.9 Å
skewness	0.336
kurtosis	-0.409
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	16050000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.951

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	L-asparaginase II protein
formula_weight	36161.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6039

GIDPFTMTNPVTVEVTRGLLVESRHRGAVAVVDGDGKLFFSLGDIDTAVFPRXACKAMQALPLVESGAADAYGFGDKELALACASHNGEEEHVALAASMLSRAGRNVEALECGAHWSMNQKVLIQQARSLDAPTALHNNCSGKHAGFICACCHRDIDPKGYVGYEHPLQVEIRAVMERLTGAVLGAESCGTDGCSIPTYAMPLRNLAHGFARMATGTGLEPLRAKASRRLIEACMAEPFYVAGSGRACTKLMQIAPGRIFVKTGAEGVFCAAIPEKGIGISLKSEDGATRAAEAMVAATLARFFETEETVHAALMAFAAMPMRNWNGIHVGDIRATSVFSA

Source

organism	Rhizobium etli
ncbi_taxonomy_id	29449
host_organism	Escherichia coli

Entity 2 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	11

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	PROPIONAMIDE
formula_weight	73.1 kDa
src_method	man
entity_count	2

Source

organism	Rhizobium etli
ncbi_taxonomy_id	29449
host_organism	Escherichia coli

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	749

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6. Citations (1)

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length_a	61.415 Å
length_b	80.453 Å
length_c	142.715 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.400 Å
resolution_low	34.070 Å
r_factor	0.1370
r_work	0.1370
r_free	0.1830

fit	/app/data/saxs_computation/th/9thy/9thy.fit
pddf	/app/data/pr_computation/th/9thy/9thy.pr.out
profile	/app/data/saxs_computation/th/9thy/9thy.dat

ReAIV structure containing an acrylamide adduct at Cys183 and an orthoborate ester at Ser47

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Source

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)