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9qcu

Crystal structure of Rhizobium etli L-asparaginase ReAV S48A mutant

Method: X-RAY DIFFRACTION D_max: 91.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qcu
deposition_date	2025-03-05
title	Crystal structure of Rhizobium etli L-asparaginase ReAV S48A 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	28.39 Å
rg_electron	27.50 Å
i0	107606000.00
molecular_weight	77632.0 kDa
excluded_volume	95503 Å³
envelope_volume	114770 Å³
shell_volume	34553 Å³
envelope_diameter	95.1 Å
shell_rg	35.31 Å
envelope_rg	27.46 Å
shape_rg	27.52 Å
total_rg	28.16 Å
total_atoms	5414
n_residues	720
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	91.6 Å
rg_real	28.37 Å
rg_real_error	0.61 Å
i0_real	1.0760e+08
i0_real_error	1.4400e+06
rg_reciprocal	28.38 Å
i0_reciprocal	107600000.0000
total_estimate	0.8942
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.329
kurtosis	-0.459
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	19060000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.893; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.950

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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	39538.9 kDa
mutation	S48A
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6412

GIDPFTMTPSEDFVVTDRGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLARAAAKPAQALAILETEGVAGYGFDDADIALMCASHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAVCSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNLPTPAFPLDRLGRIYAKLASAADGSDAGEGQSTRCAALAHIFRAMARHPEMVAGEGRYCTMLMRAFDGALVGKLGADASYAIGVRASDATRQLGTDGALGISVKIEDGNLEMLYAVVTELLERLGIGSPDVRSQLASFHHPQRVNTMGVTTGGVSFPFKLRGSKSNVDDPRLAAVAR

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	2

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	13

Entity 4 non-polymer

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

Entity 5 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	771

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6. Citations (5)

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length_a	78.041 Å
length_b	91.340 Å
length_c	105.871 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	orthorhombic

resolution	1.400 Å
resolution_low	51.760 Å
r_factor	0.1492
r_work	0.1489
r_free	0.1787

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