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9qcy

Crystal structure of Rhizobium etli L-asparaginase ReAV S80A mutant

Method: X-RAY DIFFRACTION D_max: 120.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qcy
deposition_date	2025-03-05
title	Crystal structure of Rhizobium etli L-asparaginase ReAV S80A mutant
keywords	Rhizobium etli; amidohydrolases; L-asparaginases; site-directed mutagenesis, 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	38.47 Å
rg_electron	37.84 Å
i0	379789000.00
molecular_weight	150410.0 kDa
excluded_volume	184960 Å³
envelope_volume	237440 Å³
shell_volume	51189 Å³
envelope_diameter	125.3 Å
shell_rg	44.94 Å
envelope_rg	37.10 Å
shape_rg	37.85 Å
total_rg	38.20 Å
total_atoms	10491
n_residues	1390
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	120.2 Å
rg_real	38.36 Å
rg_real_error	0.94 Å
i0_real	3.7980e+08
i0_real_error	6.2010e+06
rg_reciprocal	38.44 Å
i0_reciprocal	379800000.0000
total_estimate	0.8354
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.8 Å
skewness	0.157
kurtosis	-0.644
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	124800000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.952; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	L-asparaginase II
formula_weight	39570.9 kDa
mutation	S80A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	11594

GIDPFTMTPSEDFVVTDRGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLARSAAKPAQALAILETEGVAGYGFDDADIALMCAAHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAVCSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNLPTPAFPLDRLGRIYAKLASAADGSDAGEGQSTRCAALAHIFRAMARHPEMVAGEGRYCTMLMRAFDGALVGKLGADASYAIGVRASDATRQLGTDGALGISVKIEDGNLEMLYAVVTELLERLGIGSPDVRSQLASFHHPQRVNTMGVTTGGVSFPFKLRGSKSNVDDPRLAAVAR

Source

organism	Rhizobium etli
ncbi_taxonomy_id	29449
host_organism	Escherichia coli

Entity 2 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	30

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	911

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6. Citations (5)

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length_a	78.056 Å
length_b	91.482 Å
length_c	104.311 Å
angle_alpha	90.00 °
angle_beta	105.61 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.700 Å
resolution_low	53.660 Å
r_factor	0.2059
r_work	0.2053
r_free	0.2481

fit	/app/data/saxs_computation/qc/9qcy/9qcy.fit
pddf	/app/data/pr_computation/qc/9qcy/9qcy.pr.out
profile	/app/data/saxs_computation/qc/9qcy/9qcy.dat