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9ufr

Crystal structure of L-asparaginase from Thermococcus Sibiricus double mutation D54G/T56Q

Method: X-RAY DIFFRACTION D_max: 70.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ufr
deposition_date	2025-04-10
title	Crystal structure of L-asparaginase from Thermococcus Sibiricus double mutation D54G/T56Q
keywords	L-asparaginase, hyperthermophilic enzyme, thermo-L-asparaginase, TsAI, point mutant, double mutation, 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	21.70 Å
rg_electron	20.69 Å
i0	20638900.00
molecular_weight	36041.0 kDa
excluded_volume	45866 Å³
envelope_volume	53368 Å³
shell_volume	21649 Å³
envelope_diameter	71.0 Å
shell_rg	27.23 Å
envelope_rg	21.05 Å
shape_rg	20.68 Å
total_rg	21.63 Å
total_atoms	2529
n_residues	329
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	70.5 Å
rg_real	21.68 Å
rg_real_error	0.44 Å
i0_real	2.0640e+07
i0_real_error	2.9260e+05
rg_reciprocal	21.68 Å
i0_reciprocal	20640000.0000
total_estimate	0.8903
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	25.3 Å
skewness	0.354
kurtosis	-0.327
angular_range	— – 0.3650 Å⁻¹
current_alpha	0.0000
highest_alpha	6290000.0000
n_real_points	68
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.862; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.995

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	asparaginase
formula_weight	36655.9 kDa
ec_number	3.5.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2796

MKKLLIIGTGGTIASAKTEQGYKSVLKIDEILKLAKIKLENGYKIDSTNIMNIGSQLIHPEDWEIIAKEVFKALDDYDGIIITHGTDTLAYTASMLSFMIKNPNKPIVLTGSMLPITENGSDAPRNIRTAIKFAMEDVAGVFVAFMDKIMLGCRTSKVRTLGLNAFMSINYPDVAYVKGEKILYNIPKEKFQPNGSPELDTKYEPRVVVLRVTPGLGGEIIDAVLDAGYKGIVLEGYGAGGLPYRKSNLLSKIKEITPKIPVIMTTQALYDGVDMRKYEVGRKALETGIIPAKDMTKEATITKLMWALGHTKDVEKIREIMHTNYVNEIKS

Source

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

Entity 2 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	GLYCINE
formula_weight	75.1 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	220

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6. Citations (1)

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length_a	45.013 Å
length_b	57.447 Å
length_c	130.649 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	22.700 Å
r_factor	0.1774
r_work	0.1750
r_free	0.2253

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