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9ub5

The structure of the AglA-Arg complex

Method: X-RAY DIFFRACTION D_max: 54.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ub5
deposition_date	2025-04-02
title	The structure of the AglA-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	18.54 Å
rg_electron	17.06 Å
i0	14938700.00
molecular_weight	28248.0 kDa
excluded_volume	34923 Å³
envelope_volume	39810 Å³
shell_volume	18986 Å³
envelope_diameter	58.0 Å
shell_rg	23.79 Å
envelope_rg	17.31 Å
shape_rg	17.04 Å
total_rg	18.11 Å
total_atoms	2002
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	54.6 Å
rg_real	18.38 Å
rg_real_error	0.26 Å
i0_real	1.4940e+07
i0_real_error	1.6290e+05
rg_reciprocal	18.40 Å
i0_reciprocal	14940000.0000
total_estimate	0.8220
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	53.9 Å
skewness	0.018
kurtosis	-0.469
angular_range	— – 0.4300 Å⁻¹
current_alpha	0.0000
highest_alpha	4503000.0000
n_real_points	74
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.911; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

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	2204

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 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	202

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6. Citations (1)

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length_a	76.460 Å
length_b	76.460 Å
length_c	99.690 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 43 21 2
int_tables_number	96
crystal_system	—

resolution	1.830 Å
resolution_low	36.650 Å
r_factor	0.1709
r_work	0.1683
r_free	0.2206

fit	/app/data/saxs_computation/ub/9ub5/9ub5.fit
pddf	/app/data/pr_computation/ub/9ub5/9ub5.pr.out
profile	/app/data/saxs_computation/ub/9ub5/9ub5.dat

The structure of the AglA-Arg complex

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