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9qcw

Crystal structure of Rhizobium etli L-asparaginase ReAV K51A mutant

Method: X-RAY DIFFRACTION D_max: 91.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qcw
deposition_date	2025-03-05
title	Crystal structure of Rhizobium etli L-asparaginase ReAV K51A 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	28.44 Å
rg_electron	27.54 Å
i0	105579000.00
molecular_weight	77232.0 kDa
excluded_volume	95160 Å³
envelope_volume	113880 Å³
shell_volume	34336 Å³
envelope_diameter	95.4 Å
shell_rg	35.25 Å
envelope_rg	27.44 Å
shape_rg	27.54 Å
total_rg	28.21 Å
total_atoms	5391
n_residues	716
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	91.8 Å
rg_real	28.43 Å
rg_real_error	0.73 Å
i0_real	1.0560e+08
i0_real_error	1.5060e+06
rg_reciprocal	28.44 Å
i0_reciprocal	105600000.0000
total_estimate	0.6445
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.330
kurtosis	-0.462
angular_range	— – 0.2800 Å⁻¹
current_alpha	0.0000
highest_alpha	18680000.0000
n_real_points	57
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 0.999; Sysdev: 0.242; Positv: 1.000; Valcen: 0.991; 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	39521.8 kDa
mutation	K51A, H238Y
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5946

GIDPFTMTPSEDFVVTDRGGIVENSHRVHAAVVDAKGRLLYALGNPTRMTLARSAAAPAQALAILETEGVAGYGFDDADIALMCASHSSEDRHIARTRAMLSKIKAEEADLRCGGHPSLSEMVNRSWIKQDFIPTAVCSNCSGKHVGMLAGARAIGAGTDGYHLPDHPMQGRVKRTVAELCDLDAGDVEWGTDGCNLPTPAFPLDRLGRIYAKLASAADGSDAGEGQSTRCAALAHIFRAMARYPEMVAGEGRYCTMLMRAFDGALVGKLGADASYAIGVRASDATRQLGTDGALGISVKIEDGNLEMLYAVVTELLERLGIGSPDVRSQLASFHHPQRVNTMGVTTGGVSFPFKLRGSKSNVDDPRLAAVAR

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	18

Entity 3 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

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

Entity 6 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	nat
entity_count	2

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	466

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6. Citations (5)

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length_a	78.003 Å
length_b	91.271 Å
length_c	106.112 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	1.950 Å
resolution_low	69.200 Å
r_factor	0.1819
r_work	0.1811
r_free	0.2283

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