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10li

D-Ornithine/D-lysine decarboxylase complexed with putrescine and agmatine

Method: X-RAY DIFFRACTION D_max: 88.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10li
deposition_date	2026-01-26
last_revision	2026-02-11
title	D-Ornithine/D-lysine decarboxylase complexed with putrescine and agmatine
keywords	decarboxylase, PLP-dependent, Fold type III, LYASE; LYASE
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	25.30 Å
rg_electron	24.51 Å
i0	48339300.00
molecular_weight	53391.0 kDa
excluded_volume	66496 Å³
envelope_volume	79948 Å³
shell_volume	27488 Å³
envelope_diameter	93.8 Å
shell_rg	31.48 Å
envelope_rg	24.88 Å
shape_rg	24.49 Å
total_rg	25.33 Å
total_atoms	7407
n_residues	461
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	88.9 Å
rg_real	25.34 Å
rg_real_error	0.56 Å
i0_real	4.8340e+07
i0_real_error	6.2500e+05
rg_reciprocal	25.33 Å
i0_reciprocal	48340000.0000
total_estimate	0.8516
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.8 Å
skewness	0.433
kurtosis	-0.209
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	11030000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.734; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.893; Smooth: 0.970

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Diaminopimelate decarboxylase
formula_weight	54404.3 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	8791

MTDSIMQNYNQLREQVINGDRRFQHKDGHLCFEGVDLDALARQYPTPFYVFSEPEIIRNIHEIQQAFAAHKNTKTFFASKTCSVMGVLKAIRDAGICAEANSQYEVRKCLEIGFRGDQIVFNGVVKKPADLEYAIANDLYLINVDSLYELEHIDAISRKLKKVANVCVRVEPNVPSATHAELVTAFHAKSGLDLEQAEETCRRILAMPYVHLRGLHMHVGDQVPESEPFAKATKVLVDESRRLEEVLGIKFDLINVGGGIPVPYKYDDENGDPLKDNMYAGITAQDFADAVIREVHKWRTDVEICIEPGRKVTGSAAVLLTEVSCEKRKTNYDLNGNVECHVEWKFVDAGYSVLSDSQHFDWFFYVYNASRMTAAHDAWIKLAGPLCDGGDYFHMGVKGEEFLLPKETHVGDIVAFLDAGAYTIESQTVYNNRPRTGVVMIDKNGDTRLIRREDSYEDMVKYDIYLLAAALEHHHHHH

Source

organism	Salmonella enterica subsp. enterica serovar Typhimurium
ncbi_taxonomy_id	90371
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	1,4-DIAMINOBUTANE
formula_weight	88.2 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	2

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	AGMATINE
formula_weight	130.2 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	5

Entity 8 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	743

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6. Citations (1)

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length_a	139.413 Å
length_b	50.556 Å
length_c	73.281 Å
angle_alpha	90.00 °
angle_beta	120.69 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	1.670 Å
resolution_low	36.630 Å
r_factor	0.1434
r_work	0.1415
r_free	0.1802

fit	/app/data/saxs_computation/0l/10li/10li.fit
pddf	/app/data/pr_computation/0l/10li/10li.pr.out
profile	/app/data/saxs_computation/0l/10li/10li.dat