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9ubt

The structure of the AglA-Ampn-Arg complex

Method: X-RAY DIFFRACTION D_max: 55.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ubt
deposition_date	2025-04-03
title	The structure of the AglA-Ampn-Arg complex
keywords	hydroxylase, BIOSYNTHETIC PROTEIN; BIOSYNTHETIC PROTEIN
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	18.44 Å
rg_electron	16.96 Å
i0	15123800.00
molecular_weight	28342.0 kDa
excluded_volume	34992 Å³
envelope_volume	39391 Å³
shell_volume	18848 Å³
envelope_diameter	57.3 Å
shell_rg	23.77 Å
envelope_rg	17.29 Å
shape_rg	16.94 Å
total_rg	18.01 Å
total_atoms	2007
n_residues	244
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	55.8 Å
rg_real	18.28 Å
rg_real_error	0.25 Å
i0_real	1.5120e+07
i0_real_error	1.6350e+05
rg_reciprocal	18.31 Å
i0_reciprocal	15120000.0000
total_estimate	0.8176
solution_quality	GOOD a GOOD solution
n_peaks	3
r_peak_primary	24.4 Å
skewness	0.047
kurtosis	-0.435
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	4507000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.972; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	YqcI/YcgG family protein AglA
formula_weight	30840.2 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2281

MESYLWRDSEVSRSGSGDEPFGWVPEAHSVFTERILAEEPPYPCYFGTQGQQRGNNSFSAVDTRYPDTHGPAALARSLRAYRQRAWQGPKRQTLIVFVGPAVPGAELADDHRRFWTLLDELRAYDTEPWPADVPADPSDPRWQWCFDGEPWFIFAASPAYKDRRSRDLGPCLTLVFQVRRVFEGIGGSTVAGKAAKRRVREGLARYDRIGPHPTLGDGDTSTDFKWRQYTLPDDDSVAAPDACPVRHHAAAPVLPERNAVDGSALPQPHERQRP

Source

organism	Streptomyces monomycini
ncbi_taxonomy_id	371720
host_organism	Escherichia coli

Entity 2 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	ARGININE
formula_weight	175.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	(aminomethyl)phosphonic acid
formula_weight	111.0 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	274

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6. Citations (1)

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length_a	48.168 Å
length_b	72.221 Å
length_c	75.385 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	orthorhombic

resolution	1.596 Å
resolution_low	40.070 Å
r_factor	—
r_work	0.1755
r_free	0.1970

fit	/app/data/saxs_computation/ub/9ubt/9ubt.fit
pddf	/app/data/pr_computation/ub/9ubt/9ubt.pr.out
profile	/app/data/saxs_computation/ub/9ubt/9ubt.dat