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9xg1

Crystal structure of protein-asparaginase from Amycolatopsis deserti

Method: X-RAY DIFFRACTION D_max: 82.2 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9xg1
deposition_date	2025-10-29
last_revision	2026-04-15
title	Crystal structure of protein-asparaginase from Amycolatopsis deserti
keywords	Protein asparaginase, 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	26.55 Å
rg_electron	25.45 Å
i0	104570000.00
molecular_weight	77901.0 kDa
excluded_volume	96432 Å³
envelope_volume	112740 Å³
shell_volume	35784 Å³
envelope_diameter	85.3 Å
shell_rg	33.86 Å
envelope_rg	25.74 Å
shape_rg	25.46 Å
total_rg	26.23 Å
total_atoms	5483
n_residues	753
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	82.2 Å
rg_real	26.42 Å
rg_real_error	0.46 Å
i0_real	1.0460e+08
i0_real_error	1.4790e+06
rg_reciprocal	26.46 Å
i0_reciprocal	104600000.0000
total_estimate	0.9035
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	32.9 Å
skewness	0.216
kurtosis	-0.417
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	18150000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.982

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4. Crystallography & Experiment

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5. Entities & Polymer Info (2)

Entity 1 polymer

description	Protein-asparaginase
formula_weight	82040.5 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5743

MRKHWRPAITGAILALGLALLPTPPASAASADGSWSVTPVDGGYRITLTLDKRLPARDASPELAVDGRSLGEAQESRDGRTLTLVTTDPAAAHPSSVRVAWQGVVPGTTPRSATAPTAATDVPAGTPITSAPEAAGHYGVTRADYDFGDTALQLSGLTGVPVEERAAVWVPVGASGKRPVVVFLHGREDACYDPDSGTLDNANWPCVNGLEPMPSYLGYARSAEVLASQGYVVVSVSANAIGAFDQTTASPDRGGLARGQLVMAHLDLLAKADAGTAAGMSPVLKGKLDLGNVGLMGHSRGGDGVVRAALLNAARPTPYGIRGVLPIAPIDRTRPALTDVPMAVLLPYCDGDVSNQEGQHFFEDSRYTSGTDSALKASLLMMGANHNYFNSVWTQVYGDDWDVYVDPGDPACGSSVAGNTRLTVDEQRAAGVAYTAAFFRMTLGRESAFLPMFQSGSGSAVQVGAATVLQATQSPAAQRLDVAPLQAAAGNVAFSGKVLGQYCASIAGASPQSGLPSCSDSTATSRFPSFTPVTHTTNVPATPMLHLTWANGGQMTAALPSGRYDVSRYGALTLRAAPDAGNIAADLQLTVVDGAGRTQSTTVSALSDALSPLPAGNQDLLPKTWLRTVRWPVAAMTLVDTTDIRQIRITTATATGGVLLSDLAFTTPSVGTGAPTKLPQLSVTDTTADEDAGNATVAVRLSKASSLPVTVHLQARTGAGTHITAAAQKVTIPAGQTTATVTIPIQDNSTVDASADTPYQVVLGYPTNAVTGKNTAYVTIHDDEALEHHHHHH

Source

organism	Amycolatopsis deserti
ncbi_taxonomy_id	185696
host_organism	Escherichia coli

Entity 2 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	260

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6. Citations (1)

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length_a	53.654 Å
length_b	99.750 Å
length_c	114.283 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.080 Å
resolution_low	48.620 Å
r_factor	0.1830
r_work	0.1799
r_free	0.2442

fit	/app/data/saxs_computation/xg/9xg1/9xg1.fit
pddf	/app/data/pr_computation/xg/9xg1/9xg1.pr.out
profile	/app/data/saxs_computation/xg/9xg1/9xg1.dat

Crystal structure of protein-asparaginase from Amycolatopsis deserti

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)