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9ufq

Crystal structure of L-asparaginase from Thermococcus Sibiricus

Method: X-RAY DIFFRACTION D_max: 71.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ufq
deposition_date	2025-04-10
title	Crystal structure of L-asparaginase from Thermococcus Sibiricus
keywords	L-asparaginase, hyperthermophilic enzyme, thermo-L-asparaginase, TsAI, 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	21.65 Å
rg_electron	20.68 Å
i0	20462800.00
molecular_weight	36014.0 kDa
excluded_volume	45859 Å³
envelope_volume	53269 Å³
shell_volume	21608 Å³
envelope_diameter	73.2 Å
shell_rg	27.39 Å
envelope_rg	21.14 Å
shape_rg	20.66 Å
total_rg	21.65 Å
total_atoms	2528
n_residues	331
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	71.5 Å
rg_real	21.64 Å
rg_real_error	0.42 Å
i0_real	2.0460e+07
i0_real_error	2.5290e+05
rg_reciprocal	21.64 Å
i0_reciprocal	20460000.0000
total_estimate	0.8831
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	24.6 Å
skewness	0.373
kurtosis	-0.291
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	6030000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.997

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	asparaginase
formula_weight	36686.9 kDa
ec_number	3.5.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2845

MKKLLIIGTGGTIASAKTEQGYKSVLKIDEILKLAKIKLENGYKIDSTNIMNIDSTLIHPEDWEIIAKEVFKALDDYDGIIITHGTDTLAYTASMLSFMIKNPNKPIVLTGSMLPITENGSDAPRNIRTAIKFAMEDVAGVFVAFMDKIMLGCRTSKVRTLGLNAFMSINYPDVAYVKGEKILYNIPKEKFQPNGSPELDTKYEPRVVVLRVTPGLGGEIIDAVLDAGYKGIVLEGYGAGGLPYRKSNLLSKIKEITPKIPVIMTTQALYDGVDMRKYEVGRKALETGIIPAKDMTKEATITKLMWALGHTKDVEKIREIMHTNYVNEIKS

Source

organism	Thermococcus sibiricus
ncbi_taxonomy_id	172049
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	251

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6. Citations (1)

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length_a	45.193 Å
length_b	57.791 Å
length_c	131.158 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 2 21 21
int_tables_number	18
crystal_system	—

resolution	1.900 Å
resolution_low	24.110 Å
r_factor	0.1694
r_work	0.1671
r_free	0.2145

fit	/app/data/saxs_computation/uf/9ufq/9ufq.fit
pddf	/app/data/pr_computation/uf/9ufq/9ufq.pr.out
profile	/app/data/saxs_computation/uf/9ufq/9ufq.dat

Crystal structure of L-asparaginase from Thermococcus Sibiricus

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