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9qct

Crystal structure of Rhizobium etli L-asparaginase ReAV R47A mutant

Method: X-RAY DIFFRACTION D_max: 130.1 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qct
deposition_date	2025-03-05
title	Crystal structure of Rhizobium etli L-asparaginase ReAV R47A 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	39.73 Å
rg_electron	39.41 Å
i0	370904000.00
molecular_weight	149390.0 kDa
excluded_volume	183950 Å³
envelope_volume	239770 Å³
shell_volume	50845 Å³
envelope_diameter	136.1 Å
shell_rg	45.19 Å
envelope_rg	38.53 Å
shape_rg	39.44 Å
total_rg	39.64 Å
total_atoms	10429
n_residues	1396
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	130.1 Å
rg_real	39.75 Å
rg_real_error	1.20 Å
i0_real	3.7090e+08
i0_real_error	7.5100e+06
rg_reciprocal	39.75 Å
i0_reciprocal	370900000.0000
total_estimate	0.6490
solution_quality	REASONABLE a REASONABLE solution
n_peaks	3
r_peak_primary	58.5 Å
skewness	0.267
kurtosis	-0.499
angular_range	— – 0.2000 Å⁻¹
current_alpha	0.0000
highest_alpha	144600000.0000
n_real_points	41
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.966; Smooth: 0.759

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	L-asparaginase II
formula_weight	39468.8 kDa
mutation	R47A
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	12159

GIDPFTMTPSEDFVVTDRGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLAASAAKPAQALAILETEGVAGYGFDDADIALMCASHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAVCSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNLPTPAFPLDRLGRIYAKLASAADGSDAGEGQSTRCAALAHIFRAMARHPEMVAGEGRYCTMLMRAFDGALVGKLGADASYAIGVRASDATRQLGTDGALGISVKIEDGNLEMLYAVVTELLERLGIGSPDVRSQLASFHHPQRVNTMGVTTGGVSFPFKLRGSKSNVDDPRLAAVAR

Source

organism	Rhizobium etli
ncbi_taxonomy_id	29449
host_organism	Escherichia coli

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	27

Entity 3 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1485

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6. Citations (5)

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length_a	78.059 Å
length_b	91.550 Å
length_c	114.462 Å
angle_alpha	90.00 °
angle_beta	96.90 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.750 Å
resolution_low	50.600 Å
r_factor	0.1712
r_work	0.1709
r_free	0.2109

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